#dbSNP_hg38_chr dbSNP_hg38_position Top SNP P-value LocusName RA 1(Reported Allele 1) nonref_allele nonref_effect OR_nonref nearest_gene_symb Study type Study Design Pubmed PMID Population_map Cohort_simple3 Sample size Analysis group Phenotype Phenotype-derived most_severe_consequence chr1 6434683 rs12074379 0.00726 ESPN T T NR NA ESPN SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr1 6434683 rs12074379 8.51E-40 NR T T NR NA ESPN SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) ESPN (ILMN_1806710) expression Expression intron_variant chr1 8708071 rs112053331 0.0009 RERE NR NR NR NA RERE SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr1 8708071 rs112053331 0.08392 NA NR NR NR NA RERE Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr1 11487007 rs2379135 0.0156 PTCHD2 NR NR NR NA DISP3 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr1 11796321 rs1801133 0.832 MTHFR A A 0.98 0.98 MTHFR SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD missense_variant chr1 14031929 rs7527934 0.00000587 PRDM2 G G 0.87 0.87 KAZN SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intergenic_region chr1 14031929 rs7527934 0.00035 PRDM2 G G 0.86 0.86 KAZN SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intergenic_region chr1 14031929 rs7527934 NR PRDM2 G G 0.97 0.97 KAZN SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intergenic_region chr1 16013965 rs1763601 1.55E-60 CLCNKA NR NR 1.22 3.38719 HSPB7 SNP-based eQTL 22685416 Caucasian MAYO 374 All CLCNKA expression in Cerebellar Expression upstream_gene_variant chr1 16013965 rs1763601 1.67E-46 CLCNKA NR NR 1.02 2.77319 HSPB7 SNP-based eQTL 22685416 Caucasian MAYO 399 All CLCNKA expression in Temporal cortex Expression upstream_gene_variant chr1 16013965 rs1763601 3.66E-25 CLCNKA NR NR 1.14 3.12677 HSPB7 SNP-based eQTL 22685416 Caucasian MAYO 197 AD CLCNKA expression in Cerebellar Expression upstream_gene_variant chr1 16013965 rs1763601 4.69E-31 CLCNKA NR NR 1.3 3.6693 HSPB7 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD CLCNKA expression in Cerebellar Expression upstream_gene_variant chr1 17283250 rs16824888 0.00398 PADI4 A A NR NA PADI3 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD 3_prime_UTR_variant chr1 17283250 rs16824888 0.0112 PADI4 A A NR NA PADI3 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD 3_prime_UTR_variant chr1 17283250 rs16824888 6.28E-87 NR A A NR NA PADI3 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group PADI4 (ILMN_1807529) expression Expression 3_prime_UTR_variant chr1 18875425 rs6695033 0.00000324 ALDH4A1 G G 2.71 NA RP13-279N23.2 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other missense_variant chr1 32614460 rs180743675 0.016 RBBP4 A A 0.44 1.55271 ZBTB8OS SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr1 32614460 rs180743675 0.328 RBBP4 A A 0.98 2.66446 ZBTB8OS SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr1 32614460 rs180743675 0.472 RBBP4 A A -0.09 0.913931 ZBTB8OS SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr1 32642799 rs9660296 0.04 RBBP4 T T 0.15 1.16183 ZBTB8OS SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr1 32642799 rs9660296 0.089 RBBP4 T T 1.7 5.47395 ZBTB8OS SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr1 32642799 rs9660296 0.779 RBBP4 T T 0.05 1.05127 ZBTB8OS SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr1 32678295 rs659867 0.053 RBBP4 C C 1.94 6.95875 RBBP4 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr1 32678295 rs659867 0.088 RBBP4 C C 0.17 1.1853 RBBP4 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr1 32678295 rs659867 0.202 RBBP4 C C 0 1 RBBP4 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr1 39858994 rs61779841 0.000544 TRIT1 A A NR NA TRIT1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr1 39858994 rs61779841 0.000737 TRIT1 A A NR NA TRIT1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intron_variant chr1 39858994 rs61779841 0.812 TRIT1 A A 1 1 TRIT1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr1 46721583 rs7519866 0.0000097 KIAA0494 G G 0.71 0.71 EFCAB14 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD upstream_gene_variant chr1 46721583 rs7519866 0.04 KIAA0494 G G 1.15 1.15 EFCAB14 SNP-based Disease risk 23565137 Asian Cohort from Japan 1870 All LOAD AD upstream_gene_variant chr1 46721583 rs7519866 0.67 KIAA0494 G G 0.9 0.9 EFCAB14 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD upstream_gene_variant chr1 48181452 rs11205449 0.386 SLC5A9 NR NR NR NA SLC5A9 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr1 49465077 rs1415985 0.0000123 NR NR NR NR NA AGBL4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr1 49719403 rs11205641 0.00000841 NR NR NR NR NA AGBL4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr1 49824429 rs4926831 0.0000123 NR NR NR NR NA AGBL4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr1 49977917 rs9659092 0.00000454 NR NR NR NR NA AGBL4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr1 50094148 rs11583200 0.0000183 NR NR NR NR NA ELAVL4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr1 53502546 rs185031519 0.0000792 GLIS1 NR NR 0.06 1.06184 GLIS1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF Ab1-42 Fluid biomarker downstream_gene_variant chr1 53502546 rs185031519 0.000106 GLIS1 NR NR 0.06 1.06184 GLIS1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF Ab1-42 Fluid biomarker downstream_gene_variant chr1 53502546 rs185031519 0.0192 GLIS1 G G 0.28 1.32313 GLIS1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1530 All AD Progression (based on CDR Score) Cognitive downstream_gene_variant chr1 53502546 rs185031519 0.0343 GLIS1 G G 1.11 3.03436 GLIS1 SNP-based Disease risk 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 74046 All AD risk AD downstream_gene_variant chr1 53502546 rs185031519 0.472 GLIS1 G G 0.01 1.01005 GLIS1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF T-tau Fluid biomarker downstream_gene_variant chr1 53502546 rs185031519 0.594 GLIS1 G G 0.01 1.01005 GLIS1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF P-tau181p Fluid biomarker downstream_gene_variant chr1 53502546 rs185031519 0.615 GLIS1 G G 0.03 1.03045 GLIS1 SNP-based Age at onset (AAO) / Survival 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 39855 AD subjects Age at onset Other downstream_gene_variant chr1 53502546 rs185031519 2.08E-08 GLIS1 G G 0.059 1.06078 GLIS1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF Ab1-42 Fluid biomarker downstream_gene_variant chr1 53502546 rs185031519 2.08E-08 GLIS1 NR NR 0.06 1.06184 GLIS1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF Ab1-42 Fluid biomarker downstream_gene_variant chr1 54011258 rs72664117 0.00000203 LDLRAD1 A A 0.67 0.67 LDLRAD1 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54021452 rs6696554 0.00000458 NR A A 0.68 0.68 LDLRAD1 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD upstream_gene_variant chr1 54021923 rs35719463 0.00000292 NR G G 0.68 0.68 LDLRAD1 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD upstream_gene_variant chr1 54022577 rs35109297 0.00000161 NR A A 0.67 0.67 TMEM59 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD upstream_gene_variant chr1 54023275 rs6703501 0.000000311 NR T T 0.65 0.65 TMEM59 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD downstream_gene_variant chr1 54026129 rs10888830 0.00000571 TMEM59 T T 0.68 0.68 TMEM59 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD downstream_gene_variant chr1 54031367 rs1547467 0.000000184 TMEM59 T T 0.65 0.65 TMEM59 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD upstream_gene_variant chr1 54073027 rs7537946 0.000000105 TCEANC2 A A 0.64 0.64 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54086202 rs7516791 0.00000115 TCEANC2 G G 0.67 0.67 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54087534 rs9651202 0.00000115 TCEANC2 T T 0.67 0.67 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54092428 rs4926619 9.09E-08 TCEANC2 T T 0.64 0.64 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54096243 rs7555099 0.00000116 TCEANC2 C C 0.67 0.67 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54097483 rs6588502 0.00000161 TCEANC2 A A 0.67 0.67 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD 3_prime_UTR_variant chr1 54102815 rs4492560 8.49E-08 TCEANC2 G G 0.64 0.64 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54106570 rs10788972 6.18E-08 TCEANC2 C C 0.64 0.64 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54108937 rs12044517 9.75E-08 TCEANC2 G G 0.64 0.64 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54110966 rs11206283 0.00000198 TCEANC2 G G 0.67 0.67 TCEANC2 SNP-based Disease risk 25663231 Caucasian ADGC 1629 All PD ADRD intron_variant chr1 54289418 rs6697414 0.0000216 SSBP3 NR NR NR NA SSBP3 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr1 54873006 rs7551288 0.028 NR NR NR 295 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left medial frontal gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.038 NR NR NR 271 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left middle frontal gyrus (BA6) Imaging intron_variant chr1 54873006 rs7551288 0.157 NR NR NR 166 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right middle frontal gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.197 NR NR NR 150 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left inferior frontal gyrus (BA47) Imaging intron_variant chr1 54873006 rs7551288 0.232 NR NR NR 4.4 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right middle frontal gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.333 NR NR NR 113 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right superior frontal gyrus (BA8) Imaging intron_variant chr1 54873006 rs7551288 0.412 NR NR NR 98 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right precentral gyrus (BA44) Imaging intron_variant chr1 54873006 rs7551288 0.447 NR NR NR 92 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left superior frontal gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.507 NR NR NR 4.08 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right sub-gyral (BA6) Imaging intron_variant chr1 54873006 rs7551288 0.562 NR NR NR 75 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left inferior frontal gyrus (BA45) Imaging intron_variant chr1 54873006 rs7551288 0.569 NR NR NR 74 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right inferior frontal gyrus (BA47) Imaging intron_variant chr1 54873006 rs7551288 0.576 NR NR NR 73 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left precentral gyrus (BA4) Imaging intron_variant chr1 54873006 rs7551288 0.614 NR NR NR 68 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left precentral gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.637 NR NR NR 65 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right sub-gyral (BA6) Imaging intron_variant chr1 54873006 rs7551288 0.663 NR NR NR 3.93 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left precentral gyrus (BA4) Imaging intron_variant chr1 54873006 rs7551288 0.708 NR NR NR 56 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left medial frontal gyrus (BA8) Imaging intron_variant chr1 54873006 rs7551288 0.717 NR NR NR 3.88 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left middle frontal gyrus (BA6) Imaging intron_variant chr1 54873006 rs7551288 0.725 NR NR NR 3.88 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left inferior frontal gyrus (BA45) Imaging intron_variant chr1 54873006 rs7551288 0.763 NR NR NR 3.84 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left inferior frontal gyrus (BA47) Imaging intron_variant chr1 54873006 rs7551288 0.766 NR NR NR 3.83 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left precentral gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.801 NR NR NR 3.8 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left medial frontal gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.857 NR NR NR 3.73 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right precentral gyrus (BA44) Imaging intron_variant chr1 54873006 rs7551288 0.942 NR NR NR 3.59 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right inferior frontal gyrus (BA47) Imaging intron_variant chr1 54873006 rs7551288 0.951 NR NR NR 3.57 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Right superior frontal gyrus (BA8) Imaging intron_variant chr1 54873006 rs7551288 0.968 NR NR NR 3.52 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left superior frontal gyrus (BA9) Imaging intron_variant chr1 54873006 rs7551288 0.984 NR NR NR 3.44 NA DHCR24 SNP-based Endophenotype 21901424 Caucasian ADNI 103 All PiB uptake in Left medial frontal gyrus (BA8) Imaging intron_variant chr1 55166109 rs1759499 0.00105 USP24 G G NR NA USP24 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr1 55166109 rs1759499 1.57E-09 USP24 G G NR NA USP24 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr1 56385014 rs11206801 6.37E-08 NR A A NR NA AC119674.2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr1 56386595 rs4431886 6.37E-08 NR C C NR NA AC119674.2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr1 57273491 rs74834332 0.000000043 DAB1 A A 0.79 2.2034 DAB1 SNP-based Endophenotype 29274321 Caucasian ADNI 305 Normal controls Logic memory delayed (LMdT) recall test Cognitive intron_variant chr1 57634035 rs1539053 0.0000071 DAB1 NR NR 0.88 0.88 DAB1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr1 66330543 rs910694 0.2 PDE4B NR NR 1.07 1.07 PDE4B SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr1 66330543 rs910694 0.3 PDE4B NR NR 1.08 1.08 PDE4B SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr1 71819228 rs522395 0.00011 NEGR1 NR NR NR NA NEGR1 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr1 71819228 rs522395 0.10689 NA NR NR NR NA NEGR1 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr1 72346757 rs2815752 0.093 NR A A 0.01 1.01005 NEGR1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr1 72346757 rs2815752 0.253 NR A A 0.96 0.96 NEGR1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr1 72346757 rs2815752 0.767 NR A A 0.99 0.99 NEGR1 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr1 72346757 rs2815752 0.902 NR A A 0.997 0.997 NEGR1 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr1 73886165 rs6701710 0.0071 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.0237 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.0263 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.0278 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.0379 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.0475 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.0581 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.0805 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.123 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.146 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.444 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.501 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.681 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD downstream_gene_variant chr1 73886165 rs6701710 0.789 CUGBP2 NR NR NR NA LRRIQ3 SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD downstream_gene_variant chr1 74525960 rs1514175 0.169 NR A A 0.004 1.00401 FPGT-TNNI3K SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr1 74525960 rs1514175 0.426 NR A A 1.03 1.03 FPGT-TNNI3K SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr1 74525960 rs1514175 0.432 NR A A 0.983 0.983 FPGT-TNNI3K SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr1 74525960 rs1514175 0.588 NR A A 0.981 0.981 FPGT-TNNI3K SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr1 83789052 rs7539409 0.00000123 TTLL7 NR NR NR NA TTLL7 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr1 83849071 rs10747407 0.0000301 TTLL7 NR NR NR NA TTLL7 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr1 89100413 rs12725861 0.000945 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD downstream_gene_variant chr1 89100413 rs12725861 0.0085 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD downstream_gene_variant chr1 89100413 rs12725861 0.016 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD downstream_gene_variant chr1 89118386 rs6428503 0.000665 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr1 89118386 rs6428503 0.00854 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr1 89118386 rs6428503 0.0117 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr1 89122697 rs10922573 0.000833 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr1 89122697 rs10922573 0.00854 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr1 89122697 rs10922573 0.0148 GBP2 NR NR NR NA GBP2 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr1 90074206 rs2813746 0.00000172 ZNF326 A A 148.1 20845521757762694238396486799702335272885473816774277910530883584 ZNF326 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intergenic_region chr1 90074206 rs2813746 0.0000105 NR A A 148.1 20845521757762694238396486799702335272885473816774277910530883584 ZNF326 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intergenic_region chr1 93055535 rs520885 0.00000504 MTF2 NR NR NR NA MTF2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr1 96479241 rs1555543 0.452 NR C C 0.97 0.97 PTBP2 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr1 96479241 rs1555543 0.535 NR C C 1.01 1.01 PTBP2 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr1 109594056 rs2301229 0.000492 GNAI3 T T NR NA GNAI3 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD 3_prime_UTR_variant chr1 109594056 rs2301229 1.45E-211 NR T T NR NA GNAI3 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) GNAI3 (ILMN_1696003) expression Expression 3_prime_UTR_variant chr1 109931820 rs7537752 0.00209 CSF1 NR NR NR NA CSF1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD downstream_gene_variant chr1 109931820 rs7537752 0.0327 CSF1 NR NR NR NA CSF1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD downstream_gene_variant chr1 109931820 rs7537752 0.0378 CSF1 NR NR NR NA CSF1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD downstream_gene_variant chr1 113380753 rs7533701 0.00000246 MAGI3 NR NR 0.358 1.43047 MAGI3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intergenic_region chr1 113380753 rs7533701 0.000337 MAGI3 NR NR 0.357 1.42904 MAGI3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intergenic_region chr1 113380753 rs7533701 0.0109 MAGI3 NR NR 0.307 1.35934 MAGI3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intergenic_region chr1 113419409 rs7552954 0.0041 MAGI3 NR NR NR NA MAGI3 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr1 113510496 rs17507884 0.00000127 MAGI3 NR NR 0.466 1.59361 MAGI3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr1 113510496 rs17507884 0.000272 MAGI3 NR NR 0.476 1.60962 MAGI3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr1 113510496 rs17507884 0.00145 MAGI3 NR NR 0.452 1.57145 MAGI3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr1 113969461 rs11102709 0.0000425 HIPK1 NR NR 2.96 2.96 HIPK1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr1 113973708 rs10108 0.0000416 HIPK1 NR NR 0.34 0.34 HIPK1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD 3_prime_UTR_variant chr1 149951049 rs6587723 0.000326 OTUD7B C C NR NA OTUD7B SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr1 149951049 rs6587723 0.0015 OTUD7B C C NR NA OTUD7B SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr1 151764400 rs1568485 0.00042 OAZ3 NR NR NR NA OAZ3 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD 5_prime_UTR_premature_start_codon_gain_variant chr1 151764400 rs1568485 0.00097 OAZ3 NR NR NR NA OAZ3 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD 5_prime_UTR_premature_start_codon_gain_variant chr1 151764400 rs1568485 0.0057 OAZ3 NR NR NR NA OAZ3 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD 5_prime_UTR_premature_start_codon_gain_variant chr1 151764400 rs1568485 0.37 OAZ3 NR NR NR NA OAZ3 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD 5_prime_UTR_premature_start_codon_gain_variant chr1 153796924 rs9426935 0.00000525 LOC343052 NR NR -96.63 1.08174e-42 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 153796924 rs9426935 0.00012 LOC343052 C C -117.61 8.36808e-52 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 153796924 rs9426935 0.0074 LOC343052 C C NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153796924 rs9426935 0.0089 LOC343052 C C -77.11 3.24752e-34 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153804190 rs4341393 0.00000525 LOC343052 NR NR -96.63 1.08174e-42 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 153804190 rs4341393 0.00012 LOC343052 C C -117.6 8.45218e-52 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 153804190 rs4341393 0.0074 LOC343052 C C NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 153804190 rs4341393 0.0089 LOC343052 C C -77.11 3.24752e-34 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 153805372 rs1139620 0.00000495 GATAD2B NR NR -96.93 8.01375e-43 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153805372 rs1139620 0.00012 GATAD2B C C -117.6 8.45218e-52 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153805372 rs1139620 0.0071 GATAD2B C C NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153805372 rs1139620 0.0085 GATAD2B C C -77.66 1.87366e-34 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153806936 rs1127091 0.00000476 GATAD2B NR NR -97.12 6.62704e-43 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153806936 rs1127091 0.00012 GATAD2B A A -117.6 8.45218e-52 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153806936 rs1127091 0.0069 GATAD2B A A NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153806936 rs1127091 0.0082 GATAD2B A A -78.02 1.30721e-34 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153807822 rs9426938 0.00000392 GATAD2B NR NR -98.03 2.66755e-43 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153807822 rs9426938 0.00012 GATAD2B C C -117.55 8.88554e-52 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153807822 rs9426938 0.0059 GATAD2B C C NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153807822 rs9426938 0.0069 GATAD2B C C -79.79 2.22661e-35 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging 3_prime_UTR_variant chr1 153820482 rs9427232 0.00000318 GATAD2B NR NR -98.95 1.06307e-43 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 153820482 rs9427232 0.00012 GATAD2B A A 117.41 978397017756068824174117462529579564512863200477184 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 153820482 rs9427232 0.0049 GATAD2B G G NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153820482 rs9427232 0.0057 GATAD2B G G -81.71 3.26436e-36 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153876520 rs7414227 0.00000278 GATAD2B NR NR -99.5 6.13337e-44 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 153876520 rs7414227 0.00016 GATAD2B G G -115.46 7.18388e-51 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 153876520 rs7414227 0.0037 GATAD2B G G NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153876520 rs7414227 0.0042 GATAD2B G G -84.58 1.85086e-37 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153881560 rs7522030 0.00000306 GATAD2B NR NR -99.72 4.92214e-44 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 153881560 rs7522030 0.00019 GATAD2B C C -114.64 1.6311e-50 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 153881560 rs7522030 0.0034 GATAD2B C C NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153881560 rs7522030 0.004 GATAD2B C C -85.67 6.22288e-38 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153904499 rs11264573 0.00000317 GATAD2B NR NR -98.93 1.08454e-43 GATAD2B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 153904499 rs11264573 0.0002 GATAD2B A A -113.67 4.30275e-50 GATAD2B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 153904499 rs11264573 0.0036 GATAD2B A A NR NA GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153904499 rs11264573 0.004 GATAD2B A A -85.1 1.10037e-37 GATAD2B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153941294 rs2252508 0.00000539 DENND4B NR NR -97.78 3.4252e-43 DENND4B SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging splice_region_variant&intron_variant chr1 153941294 rs2252508 0.0002 DENND4B G G -113.85 3.59396e-50 DENND4B SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging splice_region_variant&intron_variant chr1 153941294 rs2252508 0.0049 DENND4B G G NR NA DENND4B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging splice_region_variant&intron_variant chr1 153941294 rs2252508 0.0065 DENND4B G G -82.13 2.14484e-36 DENND4B SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging splice_region_variant&intron_variant chr1 153966654 rs11264736 0.00000376 SLC39A1 NR NR -98.69 1.37872e-43 SLC39A1 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 153966654 rs11264736 0.0001 SLC39A1 T T -119.65 1.08809e-52 SLC39A1 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 153966654 rs11264736 0.0051 SLC39A1 T T NR NA SLC39A1 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 153966654 rs11264736 0.0074 SLC39A1 T T -79.29 3.67105e-35 SLC39A1 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 154438943 rs4845622 0.0000643 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF IL6R Fluid biomarker intron_variant chr1 154438943 rs4845622 0.00293 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF IL6R Fluid biomarker intron_variant chr1 154438943 rs4845622 0.0555 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma IL6R Fluid biomarker intron_variant chr1 154438943 rs4845622 0.597 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF IL6R Fluid biomarker intron_variant chr1 154438943 rs4845622 0.82 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr1 154438943 rs4845622 0.88 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr1 154438943 rs4845622 0.89 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr1 154438943 rs4845622 0.93 IL6R NR NR -0.001 0.999 IL6R SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr1 154438943 rs4845622 1.36E-62 IL6R C C NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF IL6R Fluid biomarker intron_variant chr1 154438943 rs4845622 2.28E-36 IL6R C C NR NA IL6R SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF IL6R Fluid biomarker intron_variant chr1 154438943 rs4845622 3.29E-09 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF IL6R Fluid biomarker intron_variant chr1 154438943 rs4845622 4.44E-28 IL6R C C NR NA IL6R SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 0.000528 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 0.0157 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 0.0601 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 0.538 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 0.65 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr1 154447611 rs61812598 0.7 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr1 154447611 rs61812598 0.72 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr1 154447611 rs61812598 0.76 IL6R NR NR -0.005 0.995012 IL6R SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr1 154447611 rs61812598 1.45E-27 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 2.61E-37 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 2.67E-09 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma IL6R Fluid biomarker intron_variant chr1 154447611 rs61812598 5.91E-63 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 0.000000464 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 0.000169 IL6R NR NR 4.86 129.024 IL6R SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma IL-6r Fluid biomarker intron_variant chr1 154453788 rs4129267 0.012 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 0.0173 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 0.097 IL6R NR NR 0.001 1.001 IL6R SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr1 154453788 rs4129267 0.283 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 0.54 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr1 154453788 rs4129267 0.63 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr1 154453788 rs4129267 0.64 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr1 154453788 rs4129267 0.959 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 1.11E-26 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 1.30E-37 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF IL6R Fluid biomarker intron_variant chr1 154453788 rs4129267 1.56E-58 IL6R NR NR 0.12 1.1275 IL6R SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma IL-6r Fluid biomarker intron_variant chr1 154453788 rs4129267 2.70E-62 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF IL6R Fluid biomarker intron_variant chr1 154454494 rs2228145 0.000000464 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma IL6R Fluid biomarker missense_variant chr1 154454494 rs2228145 0.012 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF IL6R Fluid biomarker missense_variant chr1 154454494 rs2228145 0.0173 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF IL6R Fluid biomarker missense_variant chr1 154454494 rs2228145 0.283 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF IL6R Fluid biomarker missense_variant chr1 154454494 rs2228145 0.6 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker missense_variant chr1 154454494 rs2228145 0.62 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker missense_variant chr1 154454494 rs2228145 0.69 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker missense_variant chr1 154454494 rs2228145 0.85 IL6R NR NR 0.003 1.003 IL6R SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD missense_variant chr1 154454494 rs2228145 0.959 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF IL6R Fluid biomarker missense_variant chr1 154454494 rs2228145 1.11E-26 IL6R C C NR NA IL6R SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF IL6R Fluid biomarker missense_variant chr1 154454494 rs2228145 1.30E-37 IL6R C C NR NA IL6R SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF IL6R Fluid biomarker missense_variant chr1 154454494 rs2228145 2.70E-62 IL6R C C NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF IL6R Fluid biomarker missense_variant chr1 154465420 rs2229238 0.00000022 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF IL6R Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 0.000000238 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF IL6R Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 0.000000657 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF IL6R Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 0.17 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 0.55 IL6R NR NR 0.012 1.01207 IL6R SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr1 154465420 rs2229238 0.67 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 0.83 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 1.46E-11 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma IL6R Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 1.51E-09 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF IL6R Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 2.04E-08 IL6R NR NR NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF IL6R Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 2.07E-08 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF IL6R Fluid biomarker 3_prime_UTR_variant chr1 154465420 rs2229238 2.29E-14 IL6R G G NR NA IL6R SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF IL6R Fluid biomarker 3_prime_UTR_variant chr1 154544102 rs3811448 0.000000109 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF IL6R Fluid biomarker missense_variant chr1 154544102 rs3811448 0.00000049 IL6R G G NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF IL6R Fluid biomarker missense_variant chr1 154544102 rs3811448 0.000000952 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF IL6R Fluid biomarker missense_variant chr1 154544102 rs3811448 0.04 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker missense_variant chr1 154544102 rs3811448 0.11 IL6R NR NR 0.031 1.03149 TDRD10 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD missense_variant chr1 154544102 rs3811448 0.29 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker missense_variant chr1 154544102 rs3811448 0.86 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker missense_variant chr1 154544102 rs3811448 2.13E-10 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF IL6R Fluid biomarker missense_variant chr1 154544102 rs3811448 2.36E-09 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF IL6R Fluid biomarker missense_variant chr1 154544102 rs3811448 3.36E-15 IL6R G G NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF IL6R Fluid biomarker missense_variant chr1 154544102 rs3811448 7.91E-12 IL6R NR NR NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma IL6R Fluid biomarker missense_variant chr1 154544102 rs3811448 8.24E-10 IL6R G G NR NA TDRD10 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF IL6R Fluid biomarker missense_variant chr1 154572175 rs4845378 0.827 CHRNB2 T T 1.03 1.03 CHRNB2 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr1 156136394 rs505058 0.0002 LMNA NR NR 1.35 1.35 LMNA SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD missense_variant chr1 156136394 rs505058 0.0119 LMNA NR NR NR NA LMNA SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD missense_variant chr1 156136394 rs505058 0.15 LMNA NR NR NR NA LMNA SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD missense_variant chr1 156136394 rs505058 0.171 LMNA NR NR NR NA LMNA SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD missense_variant chr1 156136394 rs505058 0.261 LMNA NR NR NR NA LMNA SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD missense_variant chr1 156136394 rs505058 0.357 LMNA NR NR NR NA LMNA SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD missense_variant chr1 157834858 rs2765501 0.00000152 CD5L NR NR 0.05 1.05127 CD5L SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma CD5L Fluid biomarker intron_variant chr1 157834858 rs2765501 0.00646 CD5L NR NR 597.09 20553803470443539105282101568546374858340805974892353132193811913663431698611270693866050850066172540698028203589628320987068877929320657766222153268721210450392762498436793789453621437358839204650563436406573770522814344684927698528467609593684624516990369792 CD5L SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma CD5L Fluid biomarker intron_variant chr1 159093183 rs76576833 0.00748 AIM2 T T NR NA AIM2 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr1 159093183 rs76576833 1.82E-17 NR T T NR NA AIM2 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AIM2 (ILMN_1681301) expression Expression intron_variant chr1 161185602 rs4575098 0.000157 ADAMTS4 A A NR NA ADAMTS4 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD 3_prime_UTR_variant chr1 161185602 rs4575098 2.05E-10 ADAMTS4 A A 6.36 NA ADAMTS4 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD 3_prime_UTR_variant chr1 161185602 rs4575098 6.88E-08 ADAMTS4 A A NR NA ADAMTS4 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD 3_prime_UTR_variant chr1 165476293 rs10737511 0.00000939 LOC400794 NR NR 93.97 64662495984625947923257794161178295926784 RXRG SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 165476293 rs10737511 0.0000347 LOC400794 C C 120.34 18323057827582513744613169212539009273450782301093888 RXRG SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 165476293 rs10737511 0.00062 LOC400794 C C NR NA RXRG SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 165476293 rs10737511 0.039 LOC400794 C C 63.95 5931057271816606608158359552 RXRG SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 165478920 rs10918196 0.00000931 LOC400794 NR NR 93.94 62751430416378524043519520305202258247680 RXRG SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 165478920 rs10918196 0.0000345 LOC400794 C C 120.25 16746013958155684171462401814751122754011261342580736 RXRG SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 165478920 rs10918196 0.00061 LOC400794 C C NR NA RXRG SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 165478920 rs10918196 0.039 LOC400794 C C 63.93 5813614469141004057866928128 RXRG SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 168633624 rs10489216 0.000000844 "DPT, XCL1" G G 0.28 NA XCL1 SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3e2+e2e2 LOAD AD intergenic_region chr1 171100818 rs12076145 0.00000444 FM03 NR NR -94.94 5.86249e-42 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 171100818 rs12076145 0.0000149 FM03 G G -121.68 1.42905e-53 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171100818 rs12076145 0.00018 FM03 G G NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171100818 rs12076145 0.038 FM03 G G -63.33 3.13423e-28 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171102742 rs10911192 0.00000445 FM03 NR NR -94.89 6.16306e-42 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 171102742 rs10911192 0.000015 FM03 C C -121.62 1.51742e-53 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171102742 rs10911192 0.00018 FM03 C C NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171102742 rs10911192 0.038 FM03 C C -63.3 3.22968e-28 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171108057 rs1920149 0.00000418 FM03 NR NR -94.95 5.80415e-42 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 171108057 rs1920149 0.0000151 FM03 A A -121.46 1.78071e-53 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171108057 rs1920149 0.00018 FM03 A A NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171108057 rs1920149 0.036 FM03 A A -63.78 1.99847e-28 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171109428 rs1736556 0.000000133 FM03 NR NR -109.34 3.26769e-48 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 171109428 rs1736556 0.000000404 FM03 C C -144.41 1.92103e-63 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171109428 rs1736556 0.0000134 FM03 C C NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171109428 rs1736556 0.021 FM03 C C -69.92 4.30655e-31 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171111344 rs2075992 0.000000128 FM03 NR NR -109.5 2.78454e-48 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 171111344 rs2075992 0.000000408 FM03 C C -144.37 1.99943e-63 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171111344 rs2075992 0.0000134 FM03 C C NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171111344 rs2075992 0.02 FM03 C C -70.34 2.82961e-31 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171122735 rs1795240 0.000000346 FM03 A A -143.48 4.86887e-63 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 171122735 rs1795240 0.00000749 FM03 A A NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 171122735 rs1795240 0.011 FM03 A A -76.57 5.57278e-34 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 171122735 rs1795240 4.79E-08 FM03 NR NR -112.27 1.74485e-49 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging downstream_gene_variant chr1 171128422 rs4916390 0.00000389 FM06P NR NR -95.04 5.3046e-42 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intergenic_region chr1 171128422 rs4916390 0.0000272 FM06P T T -117.48 9.52981e-52 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr1 171128422 rs4916390 0.00024 FM06P T T NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr1 171128422 rs4916390 0.024 FM06P T T -68.66 1.51824e-30 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intergenic_region chr1 171147265 rs1795243 0.000000712 FM06P C C -141.44 3.74445e-62 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171147265 rs1795243 0.0000137 FM06P C C NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171147265 rs1795243 0.011 FM06P C C -76.81 4.3837e-34 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171147265 rs1795243 8.76E-08 FM06P NR NR -110.96 6.46672e-49 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 171149882 rs1795244 0.000000129 FM06P C C -151.07 2.46112e-66 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171149882 rs1795244 0.00000157 FM06P C C NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171149882 rs1795244 0.031 FM06P T T -66.01 2.14892e-29 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171149882 rs1795244 9.77E-08 FM06P NR NR -111.33 4.46679e-49 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 171150061 rs1736567 0.000000129 FM06P C C -151.1 2.38838e-66 FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171150061 rs1736567 0.00000158 FM06P C C NR NA FMO3 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr1 171150061 rs1736567 0.031 FM06P G G -66.02 2.12754e-29 FMO3 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr1 171150061 rs1736567 9.81E-08 FM06P NR NR -111.34 4.42234e-49 FMO3 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr1 177920345 rs543874 0.373 NR G G 0.003 1.003 SEC16B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive downstream_gene_variant chr1 177920345 rs543874 0.458 NR G G 0.979 0.979 SEC16B SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD downstream_gene_variant chr1 177920345 rs543874 0.746 NR G G 1.01 1.01 SEC16B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD downstream_gene_variant chr1 177920345 rs543874 0.883 NR G G 1.01 1.01 SEC16B SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD downstream_gene_variant chr1 178552781 rs17361286 0.000012 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.0003 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.44 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.51 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.56 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.64 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.68 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.91 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive downstream_gene_variant chr1 178552781 rs17361286 0.96 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive downstream_gene_variant chr1 178575868 rs2493864 0.000017 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intergenic_region chr1 178575868 rs2493864 0.0003 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intergenic_region chr1 178575868 rs2493864 0.46 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intergenic_region chr1 178575868 rs2493864 0.49 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intergenic_region chr1 178575868 rs2493864 0.62 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intergenic_region chr1 178575868 rs2493864 0.63 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intergenic_region chr1 178575868 rs2493864 0.76 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intergenic_region chr1 178575868 rs2493864 0.96 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intergenic_region chr1 178575868 rs2493864 0.99 "C1orf49, RALGPS2" NA NA NA NA TEX35 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intergenic_region chr1 180993146 rs1411478 0.0085 STX6 NR NR 0.04 1.04081 STX6 SNP-based eQTL 22685416 Caucasian MAYO 202 AD STX6 (ILMN_2157951) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.0117 STX6 NR NR 0.03 1.03045 STX6 SNP-based eQTL 22685416 Caucasian MAYO 399 All STX6 (ILMN_2157951) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.012 MR1 NR NR 0.08 1.08329 STX6 SNP-based eQTL 22685416 Caucasian MAYO 202 AD MR1 (ILMN_2167416) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.0427 MR1 NR NR 0.05 1.05127 STX6 SNP-based eQTL 22685416 Caucasian MAYO 374 All MR1 (ILMN_2167416) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.0448 MR1 NR NR 0.09 1.09417 STX6 SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MR1 (ILMN_2167416) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.132 STX6 NR NR -0.03 0.970446 STX6 SNP-based eQTL 22685416 Caucasian MAYO 98 PSP STX6 (ILMN_2157951) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.212 IER5 NR NR -0.04 0.960789 STX6 SNP-based eQTL 22685416 Caucasian MAYO 374 All IER5 (ILMN_1721833) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.224 MR1 NR NR 0.03 1.03045 STX6 SNP-based eQTL 22685416 Caucasian MAYO 399 All MR1 (ILMN_2167416) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.256 IER5 NR NR -0.07 0.932394 STX6 SNP-based eQTL 22685416 Caucasian MAYO 98 PSP IER5 (ILMN_1721833) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.476 IER5 NR NR 0.02 1.0202 STX6 SNP-based eQTL 22685416 Caucasian MAYO 399 All IER5 (ILMN_1721833) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.573 IER5 NR NR 0.03 1.03045 STX6 SNP-based eQTL 22685416 Caucasian MAYO 107 PSP IER5 (ILMN_1721833) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.602 MR1 NR NR 0.02 1.0202 STX6 SNP-based eQTL 22685416 Caucasian MAYO 197 AD MR1 (ILMN_2167416) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.641 STX6 NR NR -0.01 0.99005 STX6 SNP-based eQTL 22685416 Caucasian MAYO 374 All STX6 (ILMN_2157951) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.89 STX6 NR NR 0 1 STX6 SNP-based eQTL 22685416 Caucasian MAYO 107 PSP STX6 (ILMN_2157951) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.897 STX6 NR NR 0 1 STX6 SNP-based eQTL 22685416 Caucasian MAYO 197 AD STX6 (ILMN_2157951) expression in Cerebellar Expression intron_variant chr1 180993146 rs1411478 0.966 MR1 NR NR 0 1 STX6 SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MR1 (ILMN_2167416) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 0.995 IER5 NR NR 0 1 STX6 SNP-based eQTL 22685416 Caucasian MAYO 202 AD IER5 (ILMN_1721833) expression in Temporal cortex Expression intron_variant chr1 180993146 rs1411478 3.50E-11 STX6 NA NA 0.79 0.79 STX6 SNP-based Disease Risk 22685416 Caucasian "Cohorts from Europe, USA" 8851 All Progressive Supranuclear Palsy (PSP) ADRD intron_variant chr1 182469951 rs2584820 0.0001 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intron_variant chr1 182469951 rs2584820 0.03 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intron_variant chr1 182469951 rs2584820 0.07 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intron_variant chr1 182469951 rs2584820 0.19 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intron_variant chr1 182469951 rs2584820 0.2 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intron_variant chr1 182469951 rs2584820 0.76 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intron_variant chr1 182469951 rs2584820 0.89 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intron_variant chr1 182469951 rs2584820 0.98 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intron_variant chr1 182469951 rs2584820 5.90E-09 RGSL2 NA NA NA NA RGSL1 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intron_variant chr1 185453472 rs10911736 0.000000769 NR A A NR NA IVNS1ABP SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr1 193614932 rs6668266 0.00000578 "CDC73, EEF1AL12" NR NR NR NA CDC73 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr1 193627126 rs1887726 0.00000623 "CDC73, EEF1AL12" NR NR NR NA CDC73 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr1 193656103 rs6678275 0.342 NR C C 0.948 0.948 CDC73 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intergenic_region chr1 193665521 rs7550917 0.00000429 "CDC73, EEF1AL12" NR NR NR NA CDC73 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr1 194388206 rs4428865 0.000000653 LOC102723336 NR NR NR NA CDC73 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr1 196717788 rs6677604 0.0000075 CFH NR NR -1360.29 0 CFH SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma CompFactH (CFH gene) Fluid biomarker intron_variant chr1 196717788 rs6677604 9.29E-112 CFH NR NR -1567 0 CFH SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma CompFactH (CFH gene) Fluid biomarker intron_variant chr1 196871142 rs7517126 0.000601 CFHR1 NR NR -1212.74 0 CFHR4 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma CompFactH (CFHR1 gene) Fluid biomarker intron_variant chr1 196871142 rs7517126 1.46E-60 CFHR1 NR NR -1487.46 0 CFHR4 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma CompFactH (CFHR1 gene) Fluid biomarker intron_variant chr1 203186952 rs10399931 1.76E-14 CHI3L1 T T -0.58 0.559898 CHI3L1 SNP-based Cross phenotype 27832767 Caucasian Knight-ADRC 379 All CSF YKL-40 Fluid biomarker upstream_gene_variant chr1 203703739 rs145963279 0.092 ATP2B4 NR NR NR NA ATP2B4 SNP-based Disease risk 25172201 African American ADGC 816 All AD AD missense_variant chr1 206836565 rs2243170 0.000000662 IL19 A A 1.65 NA IL19 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr1 207151436 rs78363635 0.0000546 C4BPA C C NR NA C4BPA SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD upstream_gene_variant chr1 207151436 rs78363635 0.00083 C4BPA C C NR NA C4BPA SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr1 207151436 rs78363635 0.00622 C4BPA C C 1.09 1.09 C4BPA SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD upstream_gene_variant chr1 207151436 rs78363635 0.0103 C4BPA C C 1.08 1.08 C4BPA SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD upstream_gene_variant chr1 207151436 rs78363635 0.205 C4BPA C C 1 1 C4BPA SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD upstream_gene_variant chr1 207151436 rs78363635 0.742 C4BPA C C 0.96 0.96 C4BPA SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD upstream_gene_variant chr1 207505962 rs4844600 0.000000422 CR1 NR NR 1.17 1.17 CR1 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD synonymous_variant chr1 207512441 rs4266886 0.002 CR1 NR NR -0.09 NA CR1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr1 207518704 rs6656401 0.00000018 CR1 NR NR 1.27 1.27 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 7349 All AD AD intron_variant chr1 207518704 rs6656401 0.00000018 CR1 NR NR 1.38 1.38 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 4129 APOE-e4 carrier AD AD intron_variant chr1 207518704 rs6656401 0.00000037 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in intra-locular white matter (WHMT) Expression intron_variant chr1 207518704 rs6656401 0.00000065 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in intra-locular white matter (WHMT) Expression intron_variant chr1 207518704 rs6656401 0.000000849 CR1 NR NR 1.17 1.17 CR1 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD intron_variant chr1 207518704 rs6656401 0.000027 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in hippocampus (HIPP) Expression intron_variant chr1 207518704 rs6656401 0.00063 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in intra-locular white matter (WHMT) Expression intron_variant chr1 207518704 rs6656401 0.00082 CR1 NR NR 1.16 1.16 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 7078 All AD AD intron_variant chr1 207518704 rs6656401 0.0025 CR1 NR NR 1.38 1.38 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1262 All AD AD intron_variant chr1 207518704 rs6656401 0.0037 CR1 NR NR 1.13 1.13 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 9541 APOE-e4 non-carrier AD AD intron_variant chr1 207518704 rs6656401 0.0038 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in substantia nigra (SNIG) Expression intron_variant chr1 207518704 rs6656401 0.004 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in temporal cortex (TCTX) Expression intron_variant chr1 207518704 rs6656401 0.0068 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in thalamus (THAL) Expression intron_variant chr1 207518704 rs6656401 0.008 CR1 A A 1.28 1.28 CR1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr1 207518704 rs6656401 0.00902 CR1 A A 1.38 1.38 CR1 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr1 207518704 rs6656401 0.01 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in hippocampus (HIPP) Expression intron_variant chr1 207518704 rs6656401 0.01 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in frontal cortex (FCTX) Expression intron_variant chr1 207518704 rs6656401 0.01 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in thalamus (THAL) Expression intron_variant chr1 207518704 rs6656401 0.018 "CR1,CR2" NR NR -0.01 0.99005 CR1 SNP-based Endophenotype 30805717 Caucasian MAGIC 51750 All Fasting Insulin Fluid biomarker intron_variant chr1 207518704 rs6656401 0.026 CR1 NR NR 1.23 1.23 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1535 All AD AD intron_variant chr1 207518704 rs6656401 0.03 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in frontal cortex (FCTX) Expression intron_variant chr1 207518704 rs6656401 0.04 CR1 A A 1.16 1.16 CR1 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr1 207518704 rs6656401 0.05 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in putamen (PUTM) Expression intron_variant chr1 207518704 rs6656401 0.056 CR1 NR NR 1.24 1.24 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1566 All AD AD intron_variant chr1 207518704 rs6656401 0.07 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in occipital cortex (OCTX) Expression intron_variant chr1 207518704 rs6656401 0.09 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in medulla (MEDU) Expression intron_variant chr1 207518704 rs6656401 0.09 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in temporal cortex (TCTX) Expression intron_variant chr1 207518704 rs6656401 0.11 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in temporal cortex (TCTX) Expression intron_variant chr1 207518704 rs6656401 0.11 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in cerebellar cortex (CRBL) Expression intron_variant chr1 207518704 rs6656401 0.11 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in occipital cortex (OCTX) Expression intron_variant chr1 207518704 rs6656401 0.13 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in putamen (PUTM) Expression intron_variant chr1 207518704 rs6656401 0.13 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in medulla (MEDU) Expression intron_variant chr1 207518704 rs6656401 0.14 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in substantia nigra (SNIG) Expression intron_variant chr1 207518704 rs6656401 0.15 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in substantia nigra (SNIG) Expression intron_variant chr1 207518704 rs6656401 0.21 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in occipital cortex (OCTX) Expression intron_variant chr1 207518704 rs6656401 0.227 CR1 A A 0.79 0.79 CR1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr1 207518704 rs6656401 0.27 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in hippocampus (HIPP) Expression intron_variant chr1 207518704 rs6656401 0.28 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in occipital cortex (OCTX) Expression intron_variant chr1 207518704 rs6656401 0.31 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (t2377332) expression in cerebellar cortex (CRBL) Expression intron_variant chr1 207518704 rs6656401 0.31 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in frontal cortex (FCTX) Expression intron_variant chr1 207518704 rs6656401 0.36 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in frontal cortex (FCTX) Expression intron_variant chr1 207518704 rs6656401 0.375 CR1 A A 1.24 1.24 CR1 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr1 207518704 rs6656401 0.38 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in cerebellar cortex (CRBL) Expression intron_variant chr1 207518704 rs6656401 0.39 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in temporal cortex (TCTX) Expression intron_variant chr1 207518704 rs6656401 0.42 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in putamen (PUTM) Expression intron_variant chr1 207518704 rs6656401 0.47 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in thalamus (THAL) Expression intron_variant chr1 207518704 rs6656401 0.53 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in medulla (MEDU) Expression intron_variant chr1 207518704 rs6656401 0.54 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in intra-locular white matter (WHMT) Expression intron_variant chr1 207518704 rs6656401 0.58 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in cerebellar cortex (CRBL) Expression intron_variant chr1 207518704 rs6656401 0.63 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in intra-locular white matter (WHMT) Expression intron_variant chr1 207518704 rs6656401 0.66 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in occipital cortex (OCTX) Expression intron_variant chr1 207518704 rs6656401 0.68 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in thalamus (THAL) Expression intron_variant chr1 207518704 rs6656401 0.69 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in frontal cortex (FCTX) Expression intron_variant chr1 207518704 rs6656401 0.69 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in medulla (MEDU) Expression intron_variant chr1 207518704 rs6656401 0.7 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in cerebellar cortex (CRBL) Expression intron_variant chr1 207518704 rs6656401 0.71 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in medulla (MEDU) Expression intron_variant chr1 207518704 rs6656401 0.72 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in putamen (PUTM) Expression intron_variant chr1 207518704 rs6656401 0.73 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in hippocampus (HIPP) Expression intron_variant chr1 207518704 rs6656401 0.77 CR2 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR2 (2377285) expression in putamen (PUTM) Expression intron_variant chr1 207518704 rs6656401 0.8 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in substantia nigra (SNIG) Expression intron_variant chr1 207518704 rs6656401 0.84 CR1 NR NR 1.03 1.03 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 2715 All AD AD intron_variant chr1 207518704 rs6656401 0.88 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in thalamus (THAL) Expression intron_variant chr1 207518704 rs6656401 0.91 CR1 NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1 (2377395) expression in substantia nigra (SNIG) Expression intron_variant chr1 207518704 rs6656401 0.93 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377445) expression in hippocampus (HIPP) Expression intron_variant chr1 207518704 rs6656401 0.97 CR1L NR NR NR NA CR1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CR1L (2377428) expression in temporal cortex (TCTX) Expression intron_variant chr1 207518704 rs6656401 0.98 CR1 A A 1 1 CR1 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr1 207518704 rs6656401 1.39E-17 CR1 A A NR NA CR1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr1 207518704 rs6656401 3.50E-09 CR1 NR NR 1.21 1.21 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 14431 All AD AD intron_variant chr1 207518704 rs6656401 5.70E-24 CR1 A A 1.18 1.18 CR1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr1 207518704 rs6656401 7.70E-15 CR1 A A 1.17 1.17 CR1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr1 207518704 rs6656401 7.73E-15 "CR1,CR2" NR NR 0.16 1.17351 CR1 SNP-based Endophenotype 30805717 Caucasian IGAP 54162 All AD AD intron_variant chr1 207518704 rs6656401 7.90E-11 CR1 A A 1.21 1.21 CR1 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr1 207518704 rs6656401 NR CR1 A A 1.46 1.46 CR1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr1 207518704 rs6656401 NR ZCWPW1 A A 1.44 1.44 CR1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr1 207518704 rs6656401 NR ZCWPW1 A A 1.56 1.56 CR1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr1 207577223 rs679515 0.000016 CR1 T T 1.13 1.13 CR1 SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD intron_variant chr1 207577223 rs679515 3.60E-09 CR1 T T 1.22 1.22 CR1 SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 21345 APOE-e4+ subjects AD AD intron_variant chr1 207577223 rs679515 8.85E-10 CR1 A A NR NA CR1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr1 207611623 rs3818361 0.000000085 CR1 NR NR 1.28 1.28 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 7342 All AD AD intron_variant chr1 207611623 rs3818361 0.000000089 CR1 NR NR 1.19 1.19 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 14153 All AD AD intron_variant chr1 207611623 rs3818361 0.00000029 CR1 NR NR 1.34 1.34 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 4728 APOE-e4 carrier AD AD intron_variant chr1 207611623 rs3818361 0.0000092 CR1 NR NR 1.17 1.17 CR1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr1 207611623 rs3818361 0.000061 CR1 A A 1.14 1.14 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr1 207611623 rs3818361 0.0002 CR1 A A 1.15 1.15 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr1 207611623 rs3818361 0.000671 CR1 NR NR 1.38 1.38 CR1 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr1 207611623 rs3818361 0.001 CR1 A A 1.22 1.22 CR1 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr1 207611623 rs3818361 0.0014 CR1 NR NR 1.13 1.13 CR1 SNP-based Disease risk 21460840 Caucasian GERAD 9799 All AD AD intron_variant chr1 207611623 rs3818361 0.0064 CR1 NR NR 1.12 1.12 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 9328 APOE-e4 non-carrier AD AD intron_variant chr1 207611623 rs3818361 0.0071 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intron_variant chr1 207611623 rs3818361 0.012 CR1 NR NR 1.14 1.14 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intron_variant chr1 207611623 rs3818361 0.016 CR1 NR NR 1.11 1.11 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 6811 All AD AD intron_variant chr1 207611623 rs3818361 0.017 CR1 NR NR 1.1 1.1 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intron_variant chr1 207611623 rs3818361 0.019 CR1 A A 1.23 1.23 CR1 SNP-based Disease risk 21390209 Caucasian GenADA 1574 All AD AD intron_variant chr1 207611623 rs3818361 0.0237 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr1 207611623 rs3818361 0.026 CR1 NR NR 1.26 1.26 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1224 All AD AD intron_variant chr1 207611623 rs3818361 0.027 CR1 NR NR 1.12 1.12 CR1 SNP-based Disease risk 30979435 Caucasian ADGC 6554 Age >=80 y AD AD intron_variant chr1 207611623 rs3818361 0.0273 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr1 207611623 rs3818361 0.0278 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr1 207611623 rs3818361 0.034 CR1 A A 1.44 1.44 CR1 SNP-based Disease risk 21390209 Caucasian ADNI 496 All AD AD intron_variant chr1 207611623 rs3818361 0.0379 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr1 207611623 rs3818361 0.038 CR1 NR NR 1.21 1.21 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1524 All AD AD intron_variant chr1 207611623 rs3818361 0.0509 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intron_variant chr1 207611623 rs3818361 0.0619 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intron_variant chr1 207611623 rs3818361 0.0832 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intron_variant chr1 207611623 rs3818361 0.126 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intron_variant chr1 207611623 rs3818361 0.136 CR1 A A 1.14 1.14 CR1 SNP-based Disease risk 21390209 Caucasian ADGC 1525 All AD AD intron_variant chr1 207611623 rs3818361 0.15 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr1 207611623 rs3818361 0.254 CR1 A A 0.94 0.94 CR1 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr1 207611623 rs3818361 0.408 CR1 A A 0.92 0.92 CR1 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr1 207611623 rs3818361 0.444 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intron_variant chr1 207611623 rs3818361 0.466 CR1 A A 0.94 0.94 CR1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr1 207611623 rs3818361 0.501 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intron_variant chr1 207611623 rs3818361 0.603 CR1 NR NR NR NA CR1 SNP-based Endophenotype 21390209 Caucasian "ADNI, leadC" 597 AD subjects AD Progression Cognitive intron_variant chr1 207611623 rs3818361 0.68 CR1 NR NR 1.05 1.05 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1408 All AD AD intron_variant chr1 207611623 rs3818361 0.681 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intron_variant chr1 207611623 rs3818361 0.72 CR1 NR NR 1.03 1.03 CR1 SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 2655 All AD AD intron_variant chr1 207611623 rs3818361 0.789 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intron_variant chr1 207611623 rs3818361 3.20E-12 CR1 NR NR 1.21 1.21 CR1 SNP-based Disease risk 21460840 Caucasian "ADC, EADI, GERAD" 20373 All AD AD intron_variant chr1 207611623 rs3818361 3.70E-14 CR1 NR NR 1.18 1.18 CR1 SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI, GERAD" 59716 All AD AD intron_variant chr1 207611623 rs3818361 5.41E-09 CR1 NR NR 1.21 1.21 CR1 SNP-based Disease risk 30979435 Caucasian ADGC 14867 Age 60-79 y AD AD intron_variant chr1 207612944 rs6701713 0.0000087 CR1 NR NR 1.17 1.17 CR1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr1 207612944 rs6701713 0.000088 CR1 A A 1.14 1.14 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr1 207612944 rs6701713 0.0002 CR1 A A 1.15 1.15 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr1 207612944 rs6701713 0.000717 CR1 A A -0.41 0.66365 CR1 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr1 207612944 rs6701713 0.00358 CR1 A A 1.13 1.13 CR1 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr1 207612944 rs6701713 0.00402 CR1 A A 1.13 1.13 CR1 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr1 207612944 rs6701713 0.00488 CR1 A A -0.41 0.66365 CR1 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr1 207612944 rs6701713 0.011 CR1 NR NR 1.14 1.14 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intron_variant chr1 207612944 rs6701713 0.021 CR1 NR NR 1.1 1.1 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intron_variant chr1 207612944 rs6701713 0.029 NR A A 0.08 1.08329 CR1 SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology intron_variant chr1 207612944 rs6701713 1.45E-08 CR1 A A 1.18 1.18 CR1 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr1 207612944 rs6701713 3.47E-09 CR1 A A 1.19 1.19 CR1 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr1 207612944 rs6701713 4.62E-10 CR1 A A 1.16 1.16 CR1 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr1 207612944 rs6701713 5.21E-11 CR1 A A 1.17 1.17 CR1 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr1 207613483 rs2093760 1.10E-18 CR1 A A 8.82 NA CR1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr1 207621975 rs2296160 4.24E-08 CR1 NR NR 1.18 1.18 CR1 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD missense_variant&splice_region_variant chr1 207622720 rs61822977 0.00158 CR1 NR NR -0.08 NA CR1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr1 207629207 rs4844610 3.60E-24 CR1 A A 1.17 1.17 CR1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr1 207629207 rs4844610 3.80E-10 CR1 A A 1.2 1.2 CR1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr1 207629207 rs4844610 8.20E-16 CR1 A A 1.16 1.16 CR1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr1 207630796 rs1408077 0.0000083 CR1 NR NR 1.17 1.17 CR1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr1 207630796 rs1408077 0.0001 CR1 A A 1.14 1.14 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr1 207630796 rs1408077 0.0002 CR1 A A 1.16 1.16 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr1 207630796 rs1408077 0.0099 CR1 NR NR 1.15 1.15 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intron_variant chr1 207630796 rs1408077 0.0168 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intron_variant chr1 207630796 rs1408077 0.0184 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr1 207630796 rs1408077 0.02 CR1 NR NR 1.27 1.27 CR1 SNP-based Disease risk 20558387 Caucasian ADNI 740 All AD + MCI AD intron_variant chr1 207630796 rs1408077 0.0288 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr1 207630796 rs1408077 0.03 CR1 NR NR -0.067 0.935195 CR1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Entorhinal cortex thickness Imaging intron_variant chr1 207630796 rs1408077 0.0317 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr1 207630796 rs1408077 0.036 CR1 NR NR 1.06 1.06 CR1 SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intron_variant chr1 207630796 rs1408077 0.0478 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr1 207630796 rs1408077 0.0739 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intron_variant chr1 207630796 rs1408077 0.113 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intron_variant chr1 207630796 rs1408077 0.12 CR1 NR NR -0.031 0.969476 CR1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Temporal pole cortex thickness Imaging intron_variant chr1 207630796 rs1408077 0.12 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intron_variant chr1 207630796 rs1408077 0.129 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intron_variant chr1 207630796 rs1408077 0.154 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr1 207630796 rs1408077 0.21 CR1 NR NR -0.017 0.983144 CR1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Amygdala volume Imaging intron_variant chr1 207630796 rs1408077 0.32 CR1 NR NR -0.037 0.963676 CR1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Hippocampal volume Imaging intron_variant chr1 207630796 rs1408077 0.42 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intron_variant chr1 207630796 rs1408077 0.45 CR1 NR NR 0.028 1.0284 CR1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All White matter lesion volume Imaging intron_variant chr1 207630796 rs1408077 0.474 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intron_variant chr1 207630796 rs1408077 0.558 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intron_variant chr1 207630796 rs1408077 0.867 CUGBP2 NR NR NR NA CR1 SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intron_variant chr1 207630796 rs1408077 0.98 CR1 NR NR 0 1 CR1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Parahippocampal gyrus cortex thickness Imaging intron_variant chr1 213944747 rs340849 0.00000752 NR A A 0.59 0.59 PROX1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr1 213972363 rs340883 0.000047 "LOC643330, PROX1" NR NR NR NA PROX1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr1 213974903 rs1431985 0.00042 AK092251 A A NR NA PROX1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total triglycerides (TG) Non-ADRD intron_variant chr1 213974903 rs1431985 0.000663 AK092251 A A NR NA PROX1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr1 213974903 rs1431985 0.0024 AK092251 A A 1.04 1.04 PROX1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr1 213974903 rs1431985 0.00484 AK092251 A A 1.04 1.04 PROX1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr1 213974903 rs1431985 0.655 AK092251 A A 0.98 0.98 PROX1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr1 213974903 rs1431985 0.804 AK092251 A A 1 1 PROX1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr1 213990332 rs340835 0.0000011 PROX1 NR NR NR NA PROX1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr1 218532171 rs4846486 0.00000233 NR A A NR NA TGFB2 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intergenic_region chr1 219415461 rs2791559 0.0000397 NR NR NR 2.82 2.82 ZC3H11B SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD upstream_gene_variant chr1 226568270 rs7525939 0.00000529 NR NR NR NR NA STUM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr1 226568270 rs7525939 0.000141 NR NR NR 0.58 0.58 STUM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr1 226568270 rs7525939 0.000462 NR NR NR NR NA STUM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr1 226568270 rs7525939 0.0093 NR NR NR 0.6 0.6 STUM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr1 226568270 rs7525939 0.013 NR NR NR NR NA STUM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr1 226568270 rs7525939 0.16364 NR NR NR NR NA STUM SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr1 226568270 rs7525939 0.254 NR NR NR 0.59 0.59 STUM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr1 226568270 rs7525939 0.487 NR NR NR NR NA STUM SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr1 226568270 rs7525939 0.67635 NR NR NR NR NA STUM SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr1 230710231 rs4762 4.74E-18 AGT NR NR 0.68 1.97388 AGT SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma Angiotensinogen Fluid biomarker missense_variant chr1 231708601 rs12044355 0.0000092 DISC1 NR NR NR NA TSNAX-DISC1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr1 231708601 rs12044355 0.000039 DISC1 NR NR NR NA TSNAX-DISC1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr1 231708601 rs12044355 0.00822 DISC1 NR NR NR NA TSNAX-DISC1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr1 238308776 rs9659297 0.0000136 Q0VG70_HUMAN NR NR NR NA MTRNR2L11 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intergenic_region chr1 238358337 rs11583706 0.0000236 Q0VG70 NR NR NR NA MTRNR2L11 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intergenic_region chr10 520439 rs11252926 0.00000808 DIP2C NR NR 0.72 0.72 DIP2C SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr10 3113045 rs6602024 0.208 NR A A 0.93 0.93 PFKP SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr10 3113045 rs6602024 0.218 NR A A 0.01 1.01005 PFKP SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr10 3113045 rs6602024 0.23 NR A A 0.958 0.958 PFKP SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr10 3113045 rs6602024 0.993 NR A A 0.999 0.999 PFKP SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr10 8925559 rs1273007 0.00000308 LOC338591 T T 0.68 0.68 GATA3 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intergenic_region chr10 8925559 rs1273007 0.00022 LOC338591 T T 0.81 0.81 GATA3 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intergenic_region chr10 8925559 rs1273007 0.47 LOC338591 T T 0.95 0.95 GATA3 SNP-based Disease risk 23565137 Asian Cohort from Japan 1870 All LOAD AD intergenic_region chr10 11008014 rs201119 1.52E-08 "CUGBP2, PITRM1" A A 4.02 NA CELF2 SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4e4 LOAD AD intron_variant chr10 11670966 rs12784561 0.0000851 CR595071 A A 0.92 0.92 USP6NL SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr10 11670966 rs12784561 0.000131 CR595071 A A 0.92 0.92 USP6NL SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr10 11670966 rs12784561 0.00038 CR595071 A A NR NA USP6NL SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr10 11670966 rs12784561 0.00143 CR595071 A A NR NA USP6NL SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intergenic_region chr10 11670966 rs12784561 0.182 CR595071 A A 1 1 USP6NL SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr10 11670966 rs12784561 0.35 CR595071 A A 0.93 0.93 USP6NL SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr10 11675398 rs11257238 0.0000056 "ECHDC3, LOC439951" NR NR NR NA USP6NL SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr10 11675398 rs11257238 0.0000584 ECHDC3 C C NR NA USP6NL SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD upstream_gene_variant chr10 11675398 rs11257238 1.26E-08 ECHDC3 C C 5.69 NA USP6NL SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD upstream_gene_variant chr10 11678309 rs7920721 0.00000003 "ECHDC3, USP6NL" G G 1.08 1.08 ECHDC3 SNP-based Disease risk 28183528 Multi-ethnic "ADGC, IGAP" 59556 All AD AD upstream_gene_variant chr10 11678309 rs7920721 0.00000019 ECHDC3 G G 1.08 1.08 ECHDC3 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD upstream_gene_variant chr10 11678309 rs7920721 0.000000289 ECHDC3 G G 1.07 1.07 ECHDC3 SNP-based Disease risk 25862742 Caucasian IGAP 74046 All AD AD upstream_gene_variant chr10 11678309 rs7920721 0.000002 "ECHDC3, USP6NL" G G 1.09 1.09 ECHDC3 SNP-based Disease risk 28183528 Multi-ethnic ADGC 33269 All AD AD upstream_gene_variant chr10 11678309 rs7920721 0.00126 CR595071 NR NR -0.07 NA ECHDC3 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other upstream_gene_variant chr10 11678309 rs7920721 0.0015 ECHDC3 G G 1.11 1.11 ECHDC3 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD upstream_gene_variant chr10 11678309 rs7920721 0.0026 "ECHDC3, USP6NL" G G 1.07 1.07 ECHDC3 SNP-based Disease risk 28183528 Caucasian IGAP 26287 All AD AD upstream_gene_variant chr10 11678309 rs7920721 0.0032 ECHDC3 G G 1.07 1.07 ECHDC3 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD upstream_gene_variant chr10 11678309 rs7920721 0.08 ECHDC3 G G 1.12 1.12 ECHDC3 SNP-based Disease risk 25862742 Caucasian DemGene 2015 All AD AD upstream_gene_variant chr10 11678309 rs7920721 0.12 ECHDC3 G G 1.05 1.05 ECHDC3 SNP-based Disease risk 25862742 Caucasian deCODE 67817 All AD AD upstream_gene_variant chr10 11678309 rs7920721 0.278 ECHDC3 G G 1.049 1.049 ECHDC3 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD upstream_gene_variant chr10 11678309 rs7920721 1.80E-11 ECHDC3 G G 1.08 1.08 ECHDC3 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD upstream_gene_variant chr10 11678309 rs7920721 2.30E-09 ECHDC3 G G 1.08 1.08 ECHDC3 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD upstream_gene_variant chr10 11678309 rs7920721 3.38E-08 ECHDC3 G G 1.07 1.07 ECHDC3 SNP-based Disease risk 25862742 Caucasian "deCODE, DemGene, IGAP" 143878 All AD AD upstream_gene_variant chr10 11679120 rs11257242 2.38E-08 ECHDC3 C C NR NA ECHDC3 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD upstream_gene_variant chr10 12933450 rs10906257 0.000439 CCDC3 G G NR NA CCDC3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr10 12933450 rs10906257 0.000472 CCDC3 G G NR NA CCDC3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr10 12933450 rs10906257 0.00537 CCDC3 G G 1.06 1.06 CCDC3 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr10 12933450 rs10906257 0.0058 CCDC3 G G 1.06 1.06 CCDC3 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr10 12933450 rs10906257 0.775 CCDC3 G G 1.02 1.02 CCDC3 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr10 13768427 rs72769570 0.00000809 FRMD4A A A NR NA FRMD4A SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr10 16257952 rs10508503 0.675 NR C C 0.983 0.983 PTER SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr10 16257952 rs10508503 0.693 NR C C 1.051 1.051 PTER SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr10 16514711 rs7909832 1.45E-27 PTER NR NR -0.7 0.496585 C1QL3 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD PTER expression in Cerebellar Expression splice_region_variant&intron_variant chr10 16514711 rs7909832 2.86E-29 PTER NR NR -0.81 0.444858 C1QL3 SNP-based eQTL 22685416 Caucasian MAYO 197 AD PTER expression in Cerebellar Expression splice_region_variant&intron_variant chr10 16514711 rs7909832 3.32E-81 PTER NR NR -1 0.367879 C1QL3 SNP-based eQTL 22685416 Caucasian MAYO 399 All PTER expression in Temporal cortex Expression splice_region_variant&intron_variant chr10 16514711 rs7909832 7.54E-63 PTER NR NR -0.75 0.472367 C1QL3 SNP-based eQTL 22685416 Caucasian MAYO 374 All PTER expression in Cerebellar Expression splice_region_variant&intron_variant chr10 17026252 rs12146414 0.0000137 CUBN G G NR NA CUBN SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr10 17026252 rs12146414 0.00086 CUBN G G NR NA CUBN SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr10 17026252 rs12146414 0.0067 CUBN G G NR NA CUBN SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr10 18713958 rs11015839 0.000000645 ARL5B A A NR NA ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr10 18713958 rs11015839 0.000000787 NR A A -0.12 0.88692 ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr10 18716110 rs11015860 0.000000645 NR G G NR NA ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr10 18716110 rs11015860 0.000000787 NR G G -0.12 0.88692 ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr10 18729013 rs11015939 0.000000925 NR A A -0.12 0.88692 ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr10 18746022 rs10763625 0.000000978 NR T T -0.12 0.88692 ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker upstream_gene_variant chr10 18773327 rs2493624 0.000000614 NR G G NR NA ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr10 18785532 rs2495832 0.000000925 NR G G -0.12 0.88692 ARL5B SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr10 18871100 rs16917919 0.00000767 NR G G 147.6 12643448063789860574301947840595377367444276876034483163334967296 MALRD1 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intergenic_region chr10 18871100 rs16917919 0.0000868 NR G G 147.6 12643448063789860574301947840595377367444276876034483163334967296 MALRD1 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intergenic_region chr10 20101712 rs2358839 0.0229 PLXDC2 NR NR NR NA PLXDC2 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr10 22857501 rs145301439 0.000157 ARMC3 A A NR NA ARMC3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intergenic_region chr10 22857501 rs145301439 0.000242 ARMC3 A A NR NA ARMC3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr10 22857501 rs145301439 0.127 ARMC3 A A 1 1 ARMC3 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr10 26509293 rs77131199 0.0000036 NR A A 1.48 4.39295 APBB1IP SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr10 26509293 rs77131199 0.017 NR A A 0.37 1.44773 APBB1IP SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr10 26509293 rs77131199 0.95 NR A A 0.01 1.01005 APBB1IP SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr10 28216015 rs11006923 0.00000899 MPP7 NR NR 0.63 0.63 MPP7 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intron_variant chr10 29807699 rs2986971 0.00000012 NR G G NR NA SVIL SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF Ab1-42 Fluid biomarker intergenic_region chr10 29807699 rs2986971 0.000000888 NR G G 0.08 1.08329 SVIL SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF Ab1-42 Fluid biomarker intergenic_region chr10 42845657 rs2142991 0.00000032 BMS1 NA NA 1.3 1.3 BMS1 SNP-based Disease Risk 22685416 Caucasian "Cohorts from Europe, USA" 8851 All Progressive Supranuclear Palsy (PSP) ADRD intergenic_region chr10 42845657 rs2142991 0.23 BMS1 NR NR 0.03 1.03045 BMS1 SNP-based eQTL 22685416 Caucasian MAYO 107 PSP BMS1 (ILMN_1772713) expression in Temporal cortex Expression intergenic_region chr10 42845657 rs2142991 0.456 BMS1 NR NR -0.01 0.99005 BMS1 SNP-based eQTL 22685416 Caucasian MAYO 202 AD BMS1 (ILMN_1772713) expression in Temporal cortex Expression intergenic_region chr10 42845657 rs2142991 0.726 BMS1 NR NR 0.01 1.01005 BMS1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD BMS1 (ILMN_1772713) expression in Cerebellar Expression intergenic_region chr10 42845657 rs2142991 0.802 BMS1 NR NR 0 1 BMS1 SNP-based eQTL 22685416 Caucasian MAYO 399 All BMS1 (ILMN_1772713) expression in Temporal cortex Expression intergenic_region chr10 42845657 rs2142991 0.818 BMS1 NR NR -0.01 0.99005 BMS1 SNP-based eQTL 22685416 Caucasian MAYO 98 PSP BMS1 (ILMN_1772713) expression in Cerebellar Expression intergenic_region chr10 42845657 rs2142991 0.936 BMS1 NR NR 0 1 BMS1 SNP-based eQTL 22685416 Caucasian MAYO 374 All BMS1 (ILMN_1772713) expression in Cerebellar Expression intergenic_region chr10 42984275 rs947690 0.00000862 RET NR NR NR NA RET SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker upstream_gene_variant chr10 42987816 rs1547930 0.00000943 RET NR NR NR NA RET SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr10 42988715 rs3004258 0.00000894 RET NR NR NR NA RET SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr10 44583495 rs7893928 0.0000231 NR NR NR NR NA CXCL12 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intergenic_region chr10 51285504 rs1915678 0.0000144 PRKG1 NR NR NR NA PRKG1 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr10 52058389 rs12268753 2.01E-08 PRKG1 C C 0.3 1.34986 PRKG1 SNP-based Endophenotype 29274321 Caucasian ADNI 305 Normal controls Logic memory delayed (LMdT) recall test Cognitive intron_variant chr10 57998883 rs11006002 0.00000749 IPMK NR NR 0.799 2.22332 IPMK SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intergenic_region chr10 57998883 rs11006002 0.000396 IPMK NR NR 0.815 2.25918 IPMK SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intergenic_region chr10 57998883 rs11006002 0.01 IPMK NR NR 0.753 2.12336 IPMK SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intergenic_region chr10 58178575 rs12570088 0.00000573 IPMK A A NR NA IPMK SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD intergenic_region chr10 58178575 rs12570088 0.0000657 IPMK A A NR NA IPMK SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 51009 All Crohn disease Non-ADRD intergenic_region chr10 58388932 rs2306604 0.808 TFAM G G 1.02 1.02 TFAM SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr10 60420054 rs10994336 0.025 ANK3 NR NR 1.26 1.26 ANK3 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr10 60420054 rs10994336 0.071 ANK3 NR NR 1.36 1.36 ANK3 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr10 60540625 rs1938526 0.064 ANK3 NR NR 0.76 0.76 ANK3 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr10 60540625 rs1938526 0.13 ANK3 NR NR 0.72 0.72 ANK3 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr10 61824775 rs4948288 0.0036 ARID5B NR NR 1.07 1.07 CABCOCO1 SNP-based Disease risk 21460840 Caucasian "EADI, GERAD" 20464 All AD AD upstream_gene_variant chr10 61851595 rs2588969 0.00000069 ARID5B A A 0.88 0.88 ARID5B SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intergenic_region chr10 61851595 rs2588969 0.00000114 ARID5B A A 0.88 0.88 ARID5B SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intergenic_region chr10 61851595 rs2588969 0.000778 ARID5B A A 0.93 0.93 ARID5B SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intergenic_region chr10 61851595 rs2588969 0.00105 ARID5B A A 0.93 0.93 ARID5B SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intergenic_region chr10 61851595 rs2588969 0.018 ARID5B NR NR 1.06 1.06 ARID5B SNP-based Disease risk 21460841 Caucasian "CHARGE, EADI, GERAD" 25818 All LOAD AD intergenic_region chr10 61851595 rs2588969 0.033 ARID5B NR NR 1.06 1.06 ARID5B SNP-based Disease risk 21460840 Caucasian "EADI, GERAD" 13448 All AD AD intergenic_region chr10 61851595 rs2588969 0.189 ARID5B A A 1.05 1.05 ARID5B SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intergenic_region chr10 61851595 rs2588969 0.234 ARID5B A A 1.05 1.05 ARID5B SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intergenic_region chr10 61851595 rs2588969 0.36 ARID5B NR NR 0.99 0.99 ARID5B SNP-based Disease risk 21460840 Caucasian "ADGC, GERAD" NR All AD AD intergenic_region chr10 61851595 rs2588969 0.362 ARID5B NR NR 0.99 0.99 ARID5B SNP-based Disease risk 21460841 Caucasian "ADGC, CHARGE, EADI, GERAD" 48589 All LOAD AD intergenic_region chr10 66838712 rs116950805 0.00372 CTNNA3 NR NR NR NA CTNNA3 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 66838712 rs116950805 0.41658 NA NR NR NR NA CTNNA3 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 67796974 rs41299238 0.138 DNAJC12 NR NR NR NA DNAJC12 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr10 67796974 rs41299238 0.84615 NA NR NR NR NA DNAJC12 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr10 67895498 rs10997864 0.0481 SIRT1 NR NR NR NA SIRT1 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 67895498 rs10997864 0.82118 NA NR NR NR NA SIRT1 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 67927049 rs17454621 0.0805 HERC4 NR NR NR NA HERC4 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 67927049 rs17454621 0.8012 NA NR NR NR NA HERC4 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 68140688 rs76451279 0.00867 MYPN NR NR NR NA MYPN SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 68140688 rs76451279 0.79321 NA NR NR NR NA MYPN Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 68174501 rs3814182 0.073 MYPN NR NR 1.34 1.34 MYPN SNP-based Cross phenotype 30010129 Asian Cohort from Han Chinse 475 All AD AD synonymous_variant chr10 69778536 rs4746003 0.00000595 RP11-242G20.2 NR NR 1.3 1.3 COL13A1 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD upstream_gene_variant chr10 76886778 rs2116830 0.291 NR G G 0.944 0.944 KCNMA1 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD 3_prime_UTR_variant chr10 76886778 rs2116830 0.503 NR G G 1.02 1.02 KCNMA1 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD 3_prime_UTR_variant chr10 76977837 rs16934131 0.00334 KCNMA1 NR NR NR NA KCNMA1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr10 76977837 rs16934131 0.0357 KCNMA1 NR NR NR NA KCNMA1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr10 76977837 rs16934131 0.0452 KCNMA1 NR NR NR NA KCNMA1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr10 79182863 rs810517 0.0000002 ZMIZ1 NR NR NR NA ZMIZ1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 80027909 rs12783314 0.00026 LOC219347 A A NR NA SFTPD SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr10 80027909 rs12783314 0.00153 LOC219347 A A NR NA SFTPD SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD upstream_gene_variant chr10 83868459 rs11200713 0.0000364 GHITM NR NR NR NA GHITM SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intergenic_region chr10 84032167 rs7908652 0.00000359 "C10orf99, GHITM, PCDH21, LRT1, LRT2, RGR" NR NR NR NA GHITM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr10 84032167 rs7908652 0.000092 NR NR NR 1.5 1.5 GHITM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr10 84032167 rs7908652 0.000451 "C10orf99, GHITM, PCDH21, LRT1, LRT2, RGR" NR NR NR NA GHITM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr10 84032167 rs7908652 0.00253 "C10orf99, GHITM, PCDH21, LRT1, LRT2, RGR" NR NR NR NA GHITM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr10 84032167 rs7908652 0.0106 NR NR NR 1.74 1.74 GHITM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr10 84032167 rs7908652 0.0265 "C10orf99, GHITM, PCDH21, LRT1, LRT2, RGR" NR NR NR NA GHITM SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intergenic_region chr10 84032167 rs7908652 0.03457 "GHITM, C10orf99, PCDH21, LRT2, LRT1, RGR" NR NR NR NA GHITM SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr10 84032167 rs7908652 0.0515 NR NR NR 1.38 1.38 GHITM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr10 84032167 rs7908652 0.13064 "GHITM, C10orf99, PCDH21, LRT2, LRT1, RGR" NR NR NR NA GHITM SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr10 88998030 rs1571011 0.00000032 FAS NR NR 0.04 1.04081 FAS SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma FAS Fluid biomarker intron_variant chr10 89213735 rs13500 0.162 CH25H A A 1.18 1.18 LIPA SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD 3_prime_UTR_variant chr10 89402425 rs41284944 0.0137 IFIT3 T T NR NA LIPA SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD synonymous_variant chr10 89402425 rs41284944 1.65E-13 NR T T NR NA LIPA SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group IFIT2 (ILMN_1739428) expression Expression synonymous_variant chr10 89402425 rs41284944 4.19E-39 NR T T NR NA LIPA SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group IFIT3 (ILMN_2239754) expression Expression synonymous_variant chr10 89981179 rs17129662 0.00003 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive downstream_gene_variant chr10 89981179 rs17129662 0.002 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive downstream_gene_variant chr10 89981179 rs17129662 0.00235 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive downstream_gene_variant chr10 89981179 rs17129662 0.1 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive downstream_gene_variant chr10 89981179 rs17129662 0.23 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive downstream_gene_variant chr10 89981179 rs17129662 0.48 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive downstream_gene_variant chr10 89981179 rs17129662 0.55 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive downstream_gene_variant chr10 89981179 rs17129662 0.84 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive downstream_gene_variant chr10 89981179 rs17129662 7.00E-13 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive downstream_gene_variant chr10 90029031 rs11185978 0.00002 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intergenic_region chr10 90029031 rs11185978 0.001 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intergenic_region chr10 90029031 rs11185978 0.01 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intergenic_region chr10 90029031 rs11185978 0.05 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intergenic_region chr10 90029031 rs11185978 0.36 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intergenic_region chr10 90029031 rs11185978 0.6 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intergenic_region chr10 90029031 rs11185978 0.6 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intergenic_region chr10 90029031 rs11185978 0.61 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intergenic_region chr10 90029031 rs11185978 8.90E-13 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intergenic_region chr10 90058530 rs7071717 0.000005 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intergenic_region chr10 90058530 rs7071717 0.01 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intergenic_region chr10 90058530 rs7071717 0.01 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intergenic_region chr10 90058530 rs7071717 0.04 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intergenic_region chr10 90058530 rs7071717 0.3 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intergenic_region chr10 90058530 rs7071717 0.67 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intergenic_region chr10 90058530 rs7071717 0.73 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intergenic_region chr10 90058530 rs7071717 0.9 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intergenic_region chr10 90058530 rs7071717 2.90E-12 "MPHOSPH1, HTR7" NA NA NA NA KIF20B SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intergenic_region chr10 91864915 rs2258946 0.00000066 NR G G 1.24 3.45561 TNKS2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF Ab1-42 Fluid biomarker 3_prime_UTR_variant chr10 91864915 rs2258946 0.011 NR G G 0.17 1.1853 TNKS2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker 3_prime_UTR_variant chr10 91864915 rs2258946 0.29 NR T T -0.1 0.904837 TNKS2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker 3_prime_UTR_variant chr10 92588073 rs6583826 0.00000006 "IDE, KIF11" NR NR NR NA KIF11 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr10 92677094 rs7911264 4.50E-13 HHEX NR NR NR NA HHEX SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr10 92732959 rs2497304 8.50E-09 "EXOC6, HHEX" NR NR NR NA HHEX SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr10 94890571 rs4110517 0.00003 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intergenic_region chr10 94890571 rs4110517 0.04 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intergenic_region chr10 94890571 rs4110517 0.09 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intergenic_region chr10 94890571 rs4110517 0.1 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intergenic_region chr10 94890571 rs4110517 0.18 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intergenic_region chr10 94890571 rs4110517 0.24 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intergenic_region chr10 94890571 rs4110517 0.87 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intergenic_region chr10 94890571 rs4110517 0.94 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intergenic_region chr10 94890571 rs4110517 4.70E-10 "CYP2C19, CYP2C9" NA NA NA NA CYP2C19 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intergenic_region chr10 95595157 rs498055 0.82 LOC439999 C C 0.98 0.98 ALDH18A1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD non_coding_transcript_exon_variant chr10 99673635 rs911541 0.929 ENTPD7 G G 0.99 0.99 AL133353.2 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr10 100741814 rs4509693 0.00000629 PAX2 NR NR NR NA PAX2 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr10 102863821 rs9527 3.42E-62 C10orf32 NR NR -0.45 0.637628 BORCS7 SNP-based eQTL 22685416 Caucasian MAYO 399 All C10orf32 expression in Temporal cortex Expression 3_prime_UTR_variant chr10 103410892 rs11191683 0.021 NR T T 0.19 1.20925 PDCD11 SNP-based Endophenotype 27694991 African American "CHARGE, ENIGMA" 938 African Intracranial Volume Imaging intron_variant chr10 103410892 rs11191683 0.075 NR T T 0.09 1.09417 PDCD11 SNP-based Endophenotype 27694991 Asian "CHARGE, ENIGMA" 955 Asian Intracranial Volume Imaging intron_variant chr10 103410892 rs11191683 0.174 NR T T 0.04 1.04081 PDCD11 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 2363 European Intracranial Volume Imaging intron_variant chr10 103410892 rs11191683 0.911 NR T T -0.01 0.99005 PDCD11 SNP-based Endophenotype 27694991 Hispanic "CHARGE, ENIGMA" 1605 Hispanic Intracranial Volume Imaging intron_variant chr10 103410892 rs11191683 1.10E-10 NR T T 0.06 1.06184 PDCD11 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 26577 European Intracranial Volume Imaging intron_variant chr10 103458495 rs2986017 0.314 CALHM1 A A 0.92 0.92 CALHM1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD missense_variant chr10 104845682 rs12249460 0.00345 SORCS3 A A 0.95 2.58571 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104845682 rs12249460 0.00371 SORCS3 A A -0.941 0.390237 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104845682 rs12249460 0.02 SORCS3 A A 0.14 1.15027 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 104848677 rs6584629 0.00341 SORCS3 A A 0.688 1.98973 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104848677 rs6584629 0.0036 SORCS3 A A -0.682 0.505605 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104848677 rs6584629 0.023 SORCS3 A A 0.1 1.10517 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 104850142 rs10786828 0.00463 SORCS3 NR NR NR NA SORCS3 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr10 104850142 rs10786828 0.035 SORCS3 NR NR NR NA SORCS3 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr10 104850142 rs10786828 0.0455 SORCS3 NR NR NR NA SORCS3 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr10 104853572 rs7894737 0.00435 SORCS3 NR NR NR NA SORCS3 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr10 104853572 rs7894737 0.0469 SORCS3 NR NR NR NA SORCS3 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr10 104853572 rs7894737 0.0474 SORCS3 NR NR NR NA SORCS3 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr10 104855629 rs12259189 0.00295 SORCS3 C C -0.694 0.499574 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104855629 rs12259189 0.00318 SORCS3 C C 0.687 1.98774 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104855629 rs12259189 0.0336 SORCS3 T T 0.1 1.10517 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 104856978 rs3976793 0.00287 SORCS3 A A 0.695 2.00371 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104856978 rs3976793 0.00309 SORCS3 A A -0.689 0.502078 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104856978 rs3976793 0.0343 SORCS3 A A 0.1 1.10517 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 104860546 rs112898269 0.00344 SORCS3 NR NR NR NA SORCS3 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 104860546 rs112898269 0.2997 NA NR NR NR NA SORCS3 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 104861946 rs12262245 0.00237 SORCS3 C C -0.705 0.494109 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104861946 rs12262245 0.00258 SORCS3 C C 0.697 2.00772 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104861946 rs12262245 0.0409 SORCS3 C C 0.0941 1.09867 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 104862251 rs7086583 0.00241 SORCS3 A A -0.703 0.495098 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104862251 rs7086583 0.00262 SORCS3 A A 0.696 2.00571 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 104862251 rs7086583 0.0434 SORCS3 A A 0.0929 1.09735 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 105047431 rs1670036 0.0164 SORCS3 A A 0.21 1.23368 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 105230641 rs749304 0.00066 SORCS3 A A -0.426 0.653116 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105230641 rs749304 0.00071 SORCS3 A A 0.424 1.52806 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105230641 rs749304 0.00133 SORCS3 A A -0.235 0.790571 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105230641 rs749304 0.00903 SORCS3 A A 0.159 1.17234 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105230641 rs749304 0.0391 SORCS3 A A 0.0469 1.04802 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 105234012 rs12263804 0.00067 SORCS3 C C -0.425 0.65377 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105234012 rs12263804 0.00072 SORCS3 C C 0.423 1.52653 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105234012 rs12263804 0.00134 SORCS3 C C -0.235 0.790571 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105234012 rs12263804 0.00936 SORCS3 C C 0.158 1.17117 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 105234012 rs12263804 0.0371 SORCS3 T T 0.05 1.05127 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 105253494 rs7920533 0.0135 SORCS3 A A 0.05 1.05127 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 105263632 rs3750261 0.00073 SORCS3 C C 0.413 1.51135 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD 3_prime_UTR_variant chr10 105263632 rs3750261 0.00076 SORCS3 C C -0.412 0.662324 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD 3_prime_UTR_variant chr10 105263632 rs3750261 0.00279 SORCS3 C C -0.216 0.805735 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD 3_prime_UTR_variant chr10 105263632 rs3750261 0.0465 SORCS3 T T 0.05 1.05127 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD 3_prime_UTR_variant chr10 105265270 rs10884126 0.00072 SORCS3 A A -0.414 0.661001 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD downstream_gene_variant chr10 105265270 rs10884126 0.00074 SORCS3 A A 0.413 1.51135 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD downstream_gene_variant chr10 105265270 rs10884126 0.00292 SORCS3 A A 0.215 1.23986 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD downstream_gene_variant chr10 105265270 rs10884126 0.0463 SORCS3 A A 0.05 1.05127 SORCS3 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD downstream_gene_variant chr10 106798187 rs12258738 0.0333 SORCS1 T T 0.1415 1.152 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106802250 rs12248379 0.00306 SORCS1 T T 0.08 1.08329 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106803358 rs17121613 0.00733 SORCS1 G G -0.2 0.818731 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 106803358 rs17121613 0.0111 SORCS1 T T 0.0773 1.08037 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106890416 rs4917491 0.0446 SORCS1 T T 0.0405 1.04133 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106893409 rs7076579 0.0472 SORCS1 T T 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106893725 rs7096260 0.0494 SORCS1 A A 0.0396 1.04039 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106897422 rs12356136 0.0473 SORCS1 T T 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106898839 rs7895881 0.0467 SORCS1 A A 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106899290 rs1004921 0.045 SORCS1 A A 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106936019 rs10884389 0.00982 SORCS1 C C -0.39 0.677057 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 106936019 rs10884389 0.0489 SORCS1 T T 0.0388 1.03956 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106944789 rs10786997 0.0409 SORCS1 A A 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106946264 rs11193127 0.0417 SORCS1 A A 0.0399 1.04071 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106946440 rs11193128 0.0427 SORCS1 T T 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106949608 rs10884390 0.0417 SORCS1 A A 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106950134 rs10884391 0.00724 SORCS1 A A 0.405 1.4993 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 106950134 rs10884391 0.038 SORCS1 A A 0.0406 1.04144 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106950369 rs10786998 0.00712 SORCS1 A A 0.405 1.4993 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 106950369 rs10786998 0.0374 SORCS1 A A 0.0408 1.04164 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106952475 rs12245675 0.00942 SORCS1 C C -0.392 0.675704 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 106952475 rs12245675 0.0354 SORCS1 T T 0.0413 1.04216 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106952640 rs17276802 0.00952 SORCS1 C C -0.392 0.675704 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 106952640 rs17276802 0.0347 SORCS1 T T 0.0414 1.04227 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106957026 rs2149197 0.0268 SORCS1 C C 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 106958696 rs11193130 0.00922 SORCS1 C C 0.393 1.48142 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 106958696 rs11193130 0.0268 SORCS1 T T 0.04 1.04081 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 107102369 rs7907690 0.0498 SORCS1 A A 1.46 1.46 SORCS1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1387 All AD AD intron_variant chr10 107102369 rs7907690 0.16 SORCS1 A A 1.11 1.11 SORCS1 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1387 All Age of AD onset Other intron_variant chr10 107102983 rs4918282 0.0134 SORCS1 A A 0.07 1.07251 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 107103202 rs10787010 0.0442 SORCS1 A A 0.061 1.0629 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 107130378 rs11193209 0.006 SORCS1 C C -0.399 0.670991 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 30871 All AD AD intron_variant chr10 107130378 rs11193209 0.0384 SORCS1 T T 0.1544 1.16696 SORCS1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr10 107154687 rs601883 0.001 SORCS1 C C 3.41 3.41 SORCS1 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1374 All Age of AD onset Other intron_variant chr10 107154687 rs601883 0.07 SORCS1 C C 3.23 3.23 SORCS1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1374 All AD AD intron_variant chr10 107163360 rs600879 0.712 SORCS1 T T 1.05 1.05 SORCS1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr10 107441914 rs1903908 0.951 hCG2039140 A A 1.01 1.01 SORCS1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intergenic_region chr10 112986029 rs7079711 0.00000025 TCF7L2 NR NR NR NA TCF7L2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 112988738 rs4074720 7.80E-37 TCF7L2 NR NR NR NA TCF7L2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 112992744 rs17747324 0.0323 TCF7L2 NR NR -0.04 0.960789 TCF7L2 SNP-based Endophenotype 30805717 Caucasian IGAP 54162 All AD AD intron_variant chr10 112992744 rs17747324 7.50E-10 TCF7L2 NR NR -0.02 0.980199 TCF7L2 SNP-based Endophenotype 30805717 Caucasian MAGIC 58047 All Fasting Glucose Fluid biomarker intron_variant chr10 113022528 rs11196192 0.00000011 TCF7L2 NR NR NR NA TCF7L2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 113029318 rs7077039 1.00E-36 TCF7L2 NR NR NR NA TCF7L2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 113061490 rs11196212 1.90E-10 TCF7L2 NR NR NR NA TCF7L2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 113101545 rs10885414 0.0000087 TCF7L2 NR NR NR NA TCF7L2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 113155455 rs290483 0.00016 TCF7L2 NR NR NR NA TCF7L2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 114271014 rs676768 0.000312 VWA2 NR NR NR NA VWA2 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr10 114271014 rs676768 0.000312 VWA2 T T 0.78 0.78 VWA2 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intron_variant chr10 114271014 rs676768 0.0024 VWA2 T T 0.86 0.86 VWA2 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr10 114271014 rs676768 0.55 VWA2 T T 0.96 0.96 VWA2 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intron_variant chr10 119906261 rs2456721 0.00000494 SEC23IP NR NR 0.266 1.30474 SEC23IP SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr10 119906261 rs2456721 0.000667 SEC23IP NR NR 0.266 1.30474 SEC23IP SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr10 119906261 rs2456721 0.0026 SEC23IP NR NR 0.265 1.30343 SEC23IP SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr10 120539864 rs2182513 2.04E-29 PPAPDC1A NR NR 0.87 2.38691 PLPP4 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD PPAPDC1A expression in Cerebellar Expression intron_variant chr10 120539864 rs2182513 4.79E-82 PPAPDC1A NR NR 0.84 2.31637 PLPP4 SNP-based eQTL 22685416 Caucasian MAYO 374 All PPAPDC1A expression in Cerebellar Expression intron_variant chr10 120539864 rs2182513 5.55E-47 PPAPDC1A NR NR 0.82 2.2705 PLPP4 SNP-based eQTL 22685416 Caucasian MAYO 197 AD PPAPDC1A expression in Cerebellar Expression intron_variant chr10 120539864 rs2182513 NS PPAPDC1A NR NR 0.01 1.01005 PLPP4 SNP-based eQTL 22685416 Caucasian MAYO 399 All PPAPDC1A expression in Temporal cortex Expression intron_variant chr10 122360941 rs10510109 0.0000029 "BTBD16, PLEKHA1" NR NR NR NA PLEKHA1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr10 122360941 rs10510109 0.0000665 "BTBD16, PLEKHA1" NR NR NR NA PLEKHA1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr10 122407996 rs2421016 0.0000047 PLEKHA1 NR NR NR NA PLEKHA1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr10 122407996 rs2421016 0.00151 PLEKHA1 NR NR NR NA PLEKHA1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr10 124106508 rs7098392 0.0009 CHST15 A A NR NA CHST15 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intergenic_region chr10 124106508 rs7098392 0.00137 CHST15 A A NR NA CHST15 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr10 124418396 rs140350519 0.082 OAT NR NR NR NA OAT SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124418396 rs140350519 0.90909 NA NR NR NR NA OAT Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124484294 rs6597801 0.038 LHPP NR NR 2.32 2.32 LHPP SNP-based Cross phenotype 30010129 Asian Cohort from Han Chinse 475 All AD AD missense_variant chr10 124493728 rs60015709 0.0136 LHPP NR NR NR NA LHPP SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124493728 rs60015709 0.6014 NA NR NR NR NA LHPP Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124736183 rs11245345 0.0221 FAM53B NR NR NR NA AC068896.3 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124736183 rs11245345 0.22478 NA NR NR NR NA AC068896.3 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124771186 rs11245363 0.0723 METTL10 NR NR NR NA AC068896.3 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124771186 rs11245363 0.58042 NA NR NR NR NA AC068896.3 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124813572 rs2277263 0.124 FAM175B NR NR NR NA ABRAXAS2 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 124813572 rs2277263 0.82717 NA NR NR NR NA ABRAXAS2 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr10 126145997 rs11244841 0.00339 ADAM12 NR NR NR NA ADAM12 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr10 126145997 rs11244841 0.0438 ADAM12 NR NR NR NA ADAM12 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr10 126145997 rs11244841 0.0455 ADAM12 NR NR NR NA ADAM12 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr10 128643917 rs1575951 0.00000401 LINC01163 NR NR NR NA MKI67 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr10 129852137 rs11016976 0.001 EBF3 NR NR 1.08 1.08 EBF3 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD intron_variant chr10 129852137 rs11016976 0.024 EBF3 NR NR NR NA EBF3 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD intron_variant chr10 129852137 rs11016976 0.033 EBF3 NR NR NR NA EBF3 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD intron_variant chr10 129852137 rs11016976 0.05 EBF3 NR NR NR NA EBF3 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD intron_variant chr10 129852137 rs11016976 0.294 EBF3 NR NR NR NA EBF3 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD intron_variant chr10 129852137 rs11016976 0.966 EBF3 NR NR NR NA EBF3 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD intron_variant chr11 924904 rs10794342 0.00000445 AP2A2 C C 0.82 0.82 AP2A2 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD non_coding_transcript_exon_variant chr11 986185 rs7396366 0.00000068 AP2A2 C C 0.94 0.94 AP2A2 SNP-based Disease risk 25862742 Caucasian "deCODE, DemGene, IGAP" 143878 All AD AD intron_variant chr11 986185 rs7396366 0.00000289 AP2A2 C C 0.93 0.93 AP2A2 SNP-based Disease risk 25862742 Caucasian IGAP 74046 All AD AD intron_variant chr11 986185 rs7396366 0.21 AP2A2 C C 0.92 0.92 AP2A2 SNP-based Disease risk 25862742 Caucasian DemGene 2015 All AD AD intron_variant chr11 986185 rs7396366 0.22 AP2A2 C C 0.96 0.96 AP2A2 SNP-based Disease risk 25862742 Caucasian deCODE 67817 All AD AD intron_variant chr11 991530 rs6597951 0.0000294 AP2A2 C C NR NA AP2A2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr11 991530 rs6597951 0.000138 AP2A2 C C NR NA AP2A2 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr11 991530 rs6597951 0.17 AP2A2 C C 1 1 AP2A2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr11 2716675 rs2283202 0.0000093 KCNQ1 NR NR NR NA KCNQ1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr11 4685804 rs58655671 0.00000991 OR51E2 NR NR NR NA OR51E2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker 5_prime_UTR_variant chr11 8308071 rs4363584 0.0000306 NR NR NR 0.48 0.48 LMO1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr11 8308071 rs4363584 0.000924 NR NR NR 0.55 0.55 LMO1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr11 8308071 rs4363584 0.0129 NR NR NR 0.59 0.59 LMO1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr11 8308071 rs4363584 0.205 NR NR NR 0.72 0.72 LMO1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr11 8583046 rs4929949 0.565 NR C C 1.01 1.01 STK33 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr11 8583046 rs4929949 0.63 NR C C 1.02 1.02 STK33 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr11 8583046 rs4929949 0.709 NR C C 0.001 1.001 STK33 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr11 8583046 rs4929949 0.784 NR C C 1.01 1.01 STK33 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr11 11841863 rs12418935 0.0000011 NR A A 0.62 1.85893 USP47 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker 5_prime_UTR_variant chr11 11841863 rs12418935 0.0021 NR A A 0.26 1.29693 USP47 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker 5_prime_UTR_variant chr11 11841863 rs12418935 0.65 NR A A -0.05 0.951229 USP47 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker 5_prime_UTR_variant chr11 18074035 rs7106970 0.000588 SAAL1 C C NR NA SAAL1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr11 18074035 rs7106970 1.15E-43 NR C C NR NA SAAL1 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group SAAL1 (ENSG00000166788) expression Expression intron_variant chr11 18099100 rs11024482 0.00021 SAAL1 C C NR NA SAAL1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr11 18099100 rs11024482 2.25E-89 NR C C NR NA SAAL1 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group SAAL1 (ILMN_1658678) expression Expression intron_variant chr11 26640999 rs4497357 0.00000852 NR A A NR NA ANO3 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr11 26673295 rs4551716 0.0000083 NR C C NR NA SLC5A12 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr11 27638228 rs11030094 0.021 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 127 Normal controls 1-Year ADAS change Cognitive intron_variant chr11 27638228 rs11030094 0.048 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 127 Normal controls 2-Year Normalized Whole Brain Volume Imaging intron_variant chr11 27638228 rs11030094 0.056 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 127 Normal controls Baseline Right Normalized hippocampal volume Imaging intron_variant chr11 27638228 rs11030094 0.805 BDNF NR NR 1.62 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27645655 rs925946 0.355 BDNF NR NR 4.4 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27648561 rs10501087 0.048 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 127 Normal controls 2-Year Right Hippo Atrophy Imaging intron_variant chr11 27648561 rs10501087 0.32 BDNF NR NR 2.33 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27649363 rs2203877 0.622 BDNF NR NR 0.95 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27658369 rs6265 0.027 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 127 Normal controls 2-Year Right Hippo Atrophy Imaging missense_variant chr11 27658369 rs6265 0.428 BDNF NR NR 1.31 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD missense_variant chr11 27658369 rs6265 0.433 BDNF T T 0.93 0.93 BDNF SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD missense_variant chr11 27662970 rs11030104 0.278 BDNF NR NR 2.56 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27673917 rs11030108 0.028 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 179 MCI 1-Year ADAS change Cognitive intron_variant chr11 27673917 rs11030108 0.687 BDNF NR NR 0.75 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27679818 rs10835211 0.765 BDNF NR NR 0.54 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27704439 rs10767664 0.688 NR A A 1.02 1.02 BDNF SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr11 27704439 rs10767664 0.83 NR A A 0 1 BDNF SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr11 27704439 rs10767664 0.943 NR A A 1 1 BDNF SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr11 27710436 rs7934165 0.773 BDNF NR NR 1.8 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27723312 rs12273363 0.725 BDNF NR NR 0.41 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27724217 rs908867 0.01 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 381 All 2-Year Right Hippo Atrophy Imaging intron_variant chr11 27724217 rs908867 0.025 BDNF NR NR NR NA BDNF SNP-based Cross phenotype 24086677 Caucasian ADNI 75 AD 2-Year Right Hippo Atrophy Imaging intron_variant chr11 27724217 rs908867 0.512 BDNF NR NR 0.31 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27728178 rs1491850 0.048 BDNF NR NR NR NA BDNF SNP-based Cross phenotype 24086677 Caucasian ADNI 75 AD 2-Year Left Hippo Atrophy Imaging intron_variant chr11 27728178 rs1491850 0.6 BDNF NR NR 0.87 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 27736075 rs1157659 0.012 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 179 MCI Baseline ADAS (total 11 cognitive score) Cognitive intron_variant chr11 27736075 rs1157659 0.025 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 127 Normal controls 2-Year Left Hippo Atrophy Imaging intron_variant chr11 27736075 rs1157659 0.025 BDNF NR NR NR NA BDNF SNP-based Endophenotype 24086677 Caucasian ADNI 381 All Baseline ADAS (total 11 cognitive score) Cognitive intron_variant chr11 27736075 rs1157659 0.341 BDNF NR NR 0.5 NA BDNF SNP-based Disease risk 24086677 Caucasian ADNI 329 All AD AD intron_variant chr11 31796571 rs113859447 0.222 PAX6 NR NR NR NA PAX6 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr11 31796571 rs113859447 0.8971 NA NR NR NR NA PAX6 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr11 45688426 rs1447575 0.000000642 "CHST1, MIR7154" T T 0.51 0.51 CHST1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr11 45689102 rs1447576 0.000000546 "CHST1, MIR7154" G G 0.51 0.51 CHST1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr11 45689480 rs2666895 0.000000448 "CHST1, MIR7154" G G 0.5 0.5 CHST1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr11 45818338 rs12805422 0.000338 "C11orf94, CRY2, MAPK8IP1, PEX16" NR NR 0.06 1.06184 SLC35C1 SNP-based Cross phenotype 30805717 Caucasian IGAP 54162 All AD AD intron_variant chr11 45818338 rs12805422 9.55E-13 "C11orf94, CRY2, MAPK8IP1, PEX16" NR NR -0.02 0.980199 SLC35C1 SNP-based Cross phenotype 30805717 Caucasian MAGIC 58047 All Fasting Glucose Fluid biomarker intron_variant chr11 46890405 rs138878258 0.17 LRP4 NR NR NR NA LRP4 SNP-based Disease risk 25172201 African American ADGC 816 All AD AD missense_variant chr11 47210487 rs11039131 0.000000701 DDB2 T T 0.93 0.93 DDB2 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD upstream_gene_variant chr11 47210487 rs11039131 0.00000518 DDB2 T T 0.94 0.94 DDB2 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD upstream_gene_variant chr11 47210487 rs11039131 0.0000408 DDB2 T T NR NA DDB2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr11 47210487 rs11039131 0.0000855 DDB2 T T NR NA DDB2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total triglycerides (TG) Non-ADRD upstream_gene_variant chr11 47210487 rs11039131 0.0218 DDB2 T T 0.88 0.88 DDB2 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD upstream_gene_variant chr11 47210487 rs11039131 0.0334 DDB2 T T 1 1 DDB2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD upstream_gene_variant chr11 47272248 rs10501320 0.00000298 "ACP2,AGBL2,AMBRA1,ARFGAP2,ARHGAP1,ATG13,C1QTNF4,C11orf49,CELF1,CHRM4,CKAP5,CREB3L1,DDB2,DGKZ,F2,FAM180B,FNBP4,HARBI1,KBTBD4,LRP4,LRP4-AS1,MADD, MDK, MIR3160-1, MIR3160-2, MIR4688, MIR5582, MIR6745, MTCH2, MYBPC3, NDUFS3, NR1H3,NUP160,PACSIN3,PSMC3,PTPMT1,PTPRJ,RAPSN,SLC39A13,SNORD67,SPI1,ZNF408" NR NR 0.08 1.08329 MADD SNP-based Cross phenotype 30805717 Caucasian IGAP 54162 All AD AD 5_prime_UTR_variant chr11 47272248 rs10501320 7.11E-13 "ACP2,AGBL2,AMBRA1,ARFGAP2,ARHGAP1,ATG13,C1QTNF4,C11orf49,CELF1,CHRM4,CKAP5,CREB3L1,DDB2,DGKZ,F2,FAM180B,FNBP4,HARBI1,KBTBD4,LRP4,LRP4-AS1,MADD, MDK, MIR3160-1, MIR3160-2, MIR4688, MIR5582, MIR6745, MTCH2, MYBPC3, NDUFS3, NR1H3,NUP160,PACSIN3,PSMC3,PTPMT1,PTPRJ,RAPSN,SLC39A13,SNORD67,SPI1,ZNF408" NR NR -0.03 0.970446 MADD SNP-based Cross phenotype 30805717 Caucasian MAGIC 58047 All Fasting Glucose Fluid biomarker 5_prime_UTR_variant chr11 47343648 rs2856650 0.00000407 MYBPC3 NR NR NR NA MYBPC3 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 47349406 rs2071305 0.000000253 MYBPC3 C C NR NA MYBPC3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intron_variant chr11 47349406 rs2071305 0.00000154 MYBPC3 C C 0.93 0.93 MYBPC3 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr11 47349406 rs2071305 0.00000301 MYBPC3 C C NR NA MYBPC3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr11 47349406 rs2071305 0.00112 MYBPC3 C C 0.83 0.83 MYBPC3 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr11 47349406 rs2071305 5.62E-08 MYBPC3 C C 0.93 0.93 MYBPC3 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr11 47358789 rs3740688 0.0012 SPI1 G G 0.93 0.93 SPI1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD missense_variant chr11 47358789 rs3740688 0.00158 SPI1 NR NR 0.07 NA SPI1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other missense_variant chr11 47358789 rs3740688 5.40E-13 SPI1 G G 0.92 0.92 SPI1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD missense_variant chr11 47358789 rs3740688 9.70E-11 SPI1 G G 0.91 0.91 SPI1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD missense_variant chr11 47372754 rs896817 0.00000756 SPI1 NR NR NR NA SPI1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 47389337 rs10838702 0.00000898 "SLC39A13, SPI1" NR NR NR NA SPI1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 47398112 rs1534576 0.00000321 SLC39A13 T T NR NA SLC39A13 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr11 47398112 rs1534576 0.000746 SLC39A13 T T 1.01 1.01 SLC39A13 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr11 47398112 rs1534576 0.00703 SLC39A13 T T 1.14 1.14 SLC39A13 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr11 47398112 rs1534576 1.49E-09 SLC39A13 T T 1.08 1.08 SLC39A13 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr11 47398112 rs1534576 2.97E-08 SLC39A13 T T 1.08 1.08 SLC39A13 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr11 47398112 rs1534576 6.62E-08 SLC39A13 T T NR NA SLC39A13 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr11 47413435 rs2293576 0.24 CELF1 NR NR 1.03 1.03 SLC39A13 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD synonymous_variant chr11 47425795 rs10838709 0.0000156 PSMC3 NR NR NR NA PSMC3 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 47518145 rs4752845 0.0537 CELF1 A A 0.87 NA CELF1 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr11 47536319 rs10838725 0.000000011 CELF1 C C 1.08 1.08 CELF1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr11 47536319 rs10838725 0.000000107 CELF1 NR NR 0.14 1.15027 CELF1 SNP-based eQTL 30448613 Caucasian ADNI 763 All MYBPC3 (11725151_at) expression in blood Expression intron_variant chr11 47536319 rs10838725 0.0000067 CELF1 C C 1.08 1.08 CELF1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr11 47536319 rs10838725 0.00029 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.00036 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.00041 CELF1 C C 1.09 1.09 CELF1 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr11 47536319 rs10838725 0.00051 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.00091 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.00091 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.0011 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.0012 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.0013 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.0014 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.0023 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.0025 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.0026 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.0033 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.0039 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.004 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.0059 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.0067 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.0072 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.0079 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.0095 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.01 CELF1 C C 1.14 1.14 CELF1 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr11 47536319 rs10838725 0.019 CELF1 C C 1.14 1.14 CELF1 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr11 47536319 rs10838725 0.02 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.03 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.04 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.054 CELF1 NR NR 1.05 1.05 CELF1 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD intron_variant chr11 47536319 rs10838725 0.06 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.07 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.07 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.1 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.1 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.11 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.12 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.12 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.13 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.13 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.13 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.14 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.14 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.15 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.16 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.16 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.16 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.17 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.19 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.2 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.21 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.22 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.24 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.25 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.26 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.27 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.28 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.29 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.31 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.31 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.31 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.31 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.32 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.32 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.34 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.34 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.36 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.39 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.39 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.4 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.4 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.4 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.41 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.43 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.43 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.46 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.46 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.49 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.51 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.52 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.55 vPTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects vPTPMT1 (3372066) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.56 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.57 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.57 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.6 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.61 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.61 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.61 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.62 CELF1 C C 0.97 0.97 CELF1 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr11 47536319 rs10838725 0.65 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.65 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.66 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.66 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.67 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.67 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.67 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.68 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.68 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.68 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.7 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.71 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.72 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.72 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.74 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.75 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.76 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in medulla (MEDU) Expression intron_variant chr11 47536319 rs10838725 0.76 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.77 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.77 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.77 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.78 MTCH2 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MTCH2 (3372370) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.78 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.79 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372495) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.8 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.8 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.81 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.82 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.83 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.83 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.84 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.85 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.86 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.86 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (t3372253) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.86 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.86 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372037) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.86 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.88 CELF1 C C 0.99 0.99 CELF1 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr11 47536319 rs10838725 0.88 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 0.89 CELF1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CELF1 (3372283) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.9 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in thalamus (THAL) Expression intron_variant chr11 47536319 rs10838725 0.9 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.91 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in temporal cortex (TCTX) Expression intron_variant chr11 47536319 rs10838725 0.92 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372007) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.93 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.93 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.93 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.93 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.94 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (3372515) expression in putamen (PUTM) Expression intron_variant chr11 47536319 rs10838725 0.95 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in cerebellar cortex (CRBL) Expression intron_variant chr11 47536319 rs10838725 0.96 FNBP4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects FNBP4 (t3372459) expression in frontal cortex (FCTX) Expression intron_variant chr11 47536319 rs10838725 0.96 NDUFS3 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NDUFS3 (3329922) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.96 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in occipital cortex (OCTX) Expression intron_variant chr11 47536319 rs10838725 0.97 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in hippocampus (HIPP) Expression intron_variant chr11 47536319 rs10838725 0.98 CELF1 NR NR 1.01 1.01 CELF1 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr11 47536319 rs10838725 0.98 NUP160 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects NUP160 (3372006) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.98 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372006) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.99 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in intra-locular white matter (WHMT) Expression intron_variant chr11 47536319 rs10838725 0.99 MADD NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects MADD (3329744) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 1 KBTD4 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects KBTD4 (3372337) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 1 PTPMT1 NR NR NR NA CELF1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PTPMT1 (3372066) expression in substantia nigra (SNIG) Expression intron_variant chr11 47536319 rs10838725 NR CELF1 C C 0.99 0.99 CELF1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr11 47536319 rs10838725 NR ZCWPW1 C C 0.7 0.7 CELF1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr11 47536319 rs10838725 NR ZCWPW1 C C 1.14 1.14 CELF1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr11 47544800 rs7928842 0.0000875 CELF1 C C NR NA CELF1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr11 47544800 rs7928842 0.825 CELF1 C C 1 1 CELF1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr11 47544800 rs7928842 3.19E-24 CELF1 C C NR NA CELF1 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr11 47559891 rs11039297 0.0000124 PTPMT1 A A NR NA CELF1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr11 47559891 rs11039297 0.0000515 PTPMT1 A A NR NA CELF1 SNP-based Cross phenotype 30413934 Caucasian "GIANT, UKBB" 180423 All Waist-to-hip ratio (WHR) Non-ADRD intron_variant chr11 47559891 rs11039297 0.028 PTPMT1 A A 1 1 CELF1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr11 47578886 rs2280231 0.0000282 "DKFZp586K0821, NDUFS3" C C NR NA NDUFS3 SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD 5_prime_UTR_variant chr11 47578886 rs2280231 0.000055 NDUFS3 C C NR NA NDUFS3 SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 16559 All Type 1 diabetes (T1D) Non-ADRD 5_prime_UTR_variant chr11 47629441 rs3817334 0.007 NR T T 0.943 0.943 MTCH2 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr11 47629441 rs3817334 0.141 NR T T 0.005 1.00501 MTCH2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr11 47629441 rs3817334 0.142 NR T T 1.051 1.051 MTCH2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr11 47629441 rs3817334 0.486 NR T T 0.97 0.97 MTCH2 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr11 47641380 rs7120548 0.0011 MTCH2 NR NR 0.075 1.07788 MTCH2 SNP-based eQTL 26919393 Caucasian "UM, NACC" 364 All MTCH2 expression in Brain Expression intron_variant chr11 48311808 rs1483121 0.00258 OR4S1 NR NR 0.07 1.07251 OR4S1 SNP-based Cross phenotype 30805717 Caucasian IGAP 54162 All AD AD downstream_gene_variant chr11 48311808 rs1483121 1.66E-09 OR4S1 NR NR -0.03 0.970446 OR4S1 SNP-based Endophenotype 30805717 Caucasian MAGIC 58047 All Fasting Glucose Fluid biomarker downstream_gene_variant chr11 49980436 rs11602981 0 NR C C NR NA OR4C12 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group FOLH1 (ENSG00000086205) expression Expression downstream_gene_variant chr11 49980436 rs11602981 0.00134 FOLH1 C C NR NA OR4C12 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD downstream_gene_variant chr11 57589434 rs2848630 1.51E-59 TIMM10 NR NR -0.53 0.588605 SERPING1 SNP-based eQTL 22685416 Caucasian MAYO 374 All TIMM10 expression in Cerebellar Expression intergenic_region chr11 57589434 rs2848630 2.07E-30 TIMM10 NR NR -0.62 0.537944 SERPING1 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD TIMM10 expression in Cerebellar Expression intergenic_region chr11 57589434 rs2848630 5.23E-23 TIMM10 NR NR -0.42 0.657047 SERPING1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD TIMM10 expression in Cerebellar Expression intergenic_region chr11 57589434 rs2848630 5.48E-65 TIMM10 NR NR -0.45 0.637628 SERPING1 SNP-based eQTL 22685416 Caucasian MAYO 399 All TIMM10 expression in Temporal cortex Expression intergenic_region chr11 58587146 rs7928565 0.0247 LPXN C C NR NA ZFP91 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr11 58587146 rs7928565 7.17E-86 NR C C NR NA ZFP91 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) LPXN (ILMN_1742789) expression in peripheral blood Expression intron_variant chr11 60064457 rs1286170 0.00000901 MS4A3 NR NR NR NA MS4A3 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 60069624 rs528823 0.00000155 MS4A3 T T 0.79 0.79 MS4A3 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD synonymous_variant chr11 60071148 rs474951 0.00000125 MS4A3 G G 0.79 0.79 MS4A3 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD downstream_gene_variant chr11 60110494 rs4939311 1.29E-09 "MS4A6A, MS4A2" NR NR NR NA MS4A2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr11 60132633 rs4939312 4.96E-10 "MS4A6A, MS4A2" NR NR NR NA MS4A2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr11 60156035 rs983392 0.00000115 MS4A6A NR NR 0.15 1.16183 MS4A6A SNP-based eQTL 30448613 Caucasian ADNI 763 All MS4A4A (11751570_a_at) expression in blood Expression downstream_gene_variant chr11 60156035 rs983392 0.00000159 MS4A6A NR NR 0.179 1.19602 MS4A6A SNP-based eQTL 30448613 Caucasian ADNI 763 All MS4A4A (11732865_a_at) expression in blood Expression downstream_gene_variant chr11 60156035 rs983392 0.0000045 MS4A6A G G 0.9 0.9 MS4A6A SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD downstream_gene_variant chr11 60156035 rs983392 0.00013 MS4A4A G G 0.8 0.8 MS4A6A SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology downstream_gene_variant chr11 60156035 rs983392 0.036 MS4A4A G G 0.85 0.85 MS4A6A SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology downstream_gene_variant chr11 60156035 rs983392 0.71 MS4A6A NR NR 1.04 1.04 MS4A6A SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging downstream_gene_variant chr11 60156035 rs983392 2.34E-12 MS4A6A NR NR 0.082 1.08546 MS4A6A SNP-based eQTL 30448613 Caucasian ADNI 763 All MS4A6A (11716846_a_at) expression in blood Expression downstream_gene_variant chr11 60156035 rs983392 2.80E-11 MS4A6A G G 0.9 0.9 MS4A6A SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD downstream_gene_variant chr11 60156035 rs983392 6.10E-16 MS4A6A G G 0.9 0.9 MS4A6A SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD downstream_gene_variant chr11 60156035 rs983392 7.22E-09 MS4A6A NR NR 0.86 0.86 MS4A6A SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD downstream_gene_variant chr11 60156035 rs983392 NR MS4A4A A A 1.29 1.29 MS4A6A SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD downstream_gene_variant chr11 60156035 rs983392 NR ZCWPW1 A A 1.19 1.19 MS4A6A SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD downstream_gene_variant chr11 60156035 rs983392 NR ZCWPW1 A A 1.57 1.57 MS4A6A SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD downstream_gene_variant chr11 60169453 rs7933202 0.000016 MS4A2 C C 0.9 0.9 MS4A6A SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD downstream_gene_variant chr11 60169453 rs7933202 1.90E-19 MS4A2 C C 0.89 0.89 MS4A6A SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD downstream_gene_variant chr11 60169453 rs7933202 2.20E-15 MS4A2 C C 0.89 0.89 MS4A6A SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD downstream_gene_variant chr11 60171834 rs610932 0.000000018 MS4A6A NR NR 0.88 0.88 MS4A6A SNP-based Disease risk 21460840 Caucasian "ADC, EADI, GERAD" 20373 All AD AD 3_prime_UTR_variant chr11 60171834 rs610932 0.0000014 MS4A6A NR NR 0.87 0.87 MS4A6A SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD 3_prime_UTR_variant chr11 60171834 rs610932 0.000021 MS4A6A NR NR 0.91 0.91 MS4A6A SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI" 29544 All AD AD 3_prime_UTR_variant chr11 60171834 rs610932 0.0016 MS4A6A NR NR 0.9 0.9 MS4A6A SNP-based Disease risk 21460840 Caucasian GERAD 9799 All AD AD 3_prime_UTR_variant chr11 60171834 rs610932 0.199 MS4A6A A A 0.92 NA MS4A6A SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other 3_prime_UTR_variant chr11 60171834 rs610932 0.299 MS4A T T 0.91 0.91 MS4A6A SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD 3_prime_UTR_variant chr11 60171834 rs610932 0.799 MS4A6A T T 0.99 0.99 MS4A6A SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD 3_prime_UTR_variant chr11 60171834 rs610932 1.20E-16 MS4A6A NR NR 0.91 0.91 MS4A6A SNP-based Disease risk 21460840 Caucasian "ADGC, GERAD" NR All AD AD 3_prime_UTR_variant chr11 60171834 rs610932 1.80E-14 MS4A6A NR NR 0.9 0.9 MS4A6A SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI, GERAD" 59716 All AD AD 3_prime_UTR_variant chr11 60175284 rs662196 0.0000052 MS4A6A NR NR 0.88 0.88 MS4A6A SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr11 60175342 rs7935829 1.64E-10 MS4A6A NR NR NR NA MS4A6A SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 60175342 rs7935829 8.21E-13 MS4A6A A A NR NA MS4A6A SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr11 60178272 rs12453 1.34E-09 MS4A6A NR NR 0.86 0.86 MS4A6A SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD stop_retained_variant chr11 60179779 rs583791 0.0000053 MS4A6A NR NR 0.88 0.88 MS4A6A SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD missense_variant chr11 60190907 rs2081545 1.55E-15 MS4A6A A A -7.97 NA MS4A4A SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intergenic_region chr11 60192370 rs1834550 0.0000108 MS4A6A NR NR 0.89 0.89 MS4A4A SNP-based Disease risk 30979435 Caucasian ADGC 14677 Age 60-79 y AD AD intergenic_region chr11 60192370 rs1834550 0.000338 MS4A6A NR NR 0.86 0.86 MS4A4A SNP-based Disease risk 30979435 Caucasian ADGC 6473 Age >=80 y AD AD intergenic_region chr11 60197519 rs7116190 0.000126 MS4A6A NR NR 0.08 NA MS4A4A SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other downstream_gene_variant chr11 60201268 rs184909761 0.00000145 MS4A4E NR NR 0.86 0.86 MS4A4A SNP-based Disease risk 30979435 Caucasian ADGC 12169 Age 60-79 y AD AD 3_prime_UTR_variant chr11 60201268 rs184909761 0.000553 MS4A4E NR NR 0.85 0.85 MS4A4A SNP-based Disease risk 30979435 Caucasian ADGC 5340 Age >=80 y AD AD 3_prime_UTR_variant chr11 60204322 rs670139 0.00001 MS4A6E NR NR 1.11 1.11 MS4A4A SNP-based Disease risk 21460840 Caucasian "ADC, EADI, GERAD" 20373 All AD AD intron_variant chr11 60204322 rs670139 0.0011 MS4A6E NR NR 1.11 1.11 MS4A4A SNP-based Disease risk 21460840 Caucasian GERAD 9799 All AD AD intron_variant chr11 60204322 rs670139 0.0032 MS4A6E NR NR 1.06 1.06 MS4A4A SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI" 29544 All AD AD intron_variant chr11 60204322 rs670139 0.77 MS4A4E NR NR 0.97 0.97 MS4A4A SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr11 60204322 rs670139 0.823 MS4A6A T T 0.99 0.99 MS4A4A SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr11 60204322 rs670139 1.10E-10 MS4A6E NR NR 1.08 1.08 MS4A4A SNP-based Disease risk 21460840 Caucasian "ADGC, GERAD" NR All AD AD intron_variant chr11 60204322 rs670139 1.40E-09 MS4A6E NR NR 1.09 1.09 MS4A4A SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI, GERAD" 59716 All AD AD intron_variant chr11 60221957 rs2081547 2.19E-10 MS4A4E NR NR NR NA MS4A4A SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 60232853 rs668134 0.18 MS4A4E G G 0.84 NA MS4A4A SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr11 60234100 rs676309 0.0000063 MS4A4E NR NR 1.14 1.14 MS4A4A SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr11 60254475 rs1582763 0.003 MS4 region A A 0.92 0.92 MS4A4A SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 21345 APOE-e4+ subjects AD AD intergenic_region chr11 60254475 rs1582763 2.20E-09 MS4 region A A 0.87 0.87 MS4A4A SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD intergenic_region chr11 60254475 rs1582763 4.72E-09 MS4A6A A A NR NA MS4A4A SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intergenic_region chr11 60254847 rs10792258 0.01 MS4A T T 0.79 0.79 MS4A4A SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr11 60259140 rs4938931 1.54E-10 "MS4A4A, MS4A4E" NR NR NR NA MS4A4A SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr11 60260669 rs7108663 0.000217 MS4A6A C C NR NA MS4A4A SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intergenic_region chr11 60260669 rs7108663 1.41E-48 NR C C NR NA MS4A4A SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) MS4A6A (ILMN_2359800) expression Expression intergenic_region chr11 60266956 rs4938933 0.00054 MS4A6A NR NR 0.92 0.92 MS4A4A SNP-based Disease risk 21460841 Caucasian "CHARGE, EADI, GERAD" 25818 All LOAD AD intergenic_region chr11 60266956 rs4938933 0.0044 MS4A6A C C 0.9 0.9 MS4A4A SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intergenic_region chr11 60266956 rs4938933 0.00481 MS4A6A C C 0.9 0.9 MS4A4A SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intergenic_region chr11 60266956 rs4938933 0.323 MS4A6A C C 1.06 1.06 MS4A4A SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intergenic_region chr11 60266956 rs4938933 0.448 MS4A4A C C 0.09 1.09417 MS4A4A SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intergenic_region chr11 60266956 rs4938933 0.493 MS4A C C 1.06 1.06 MS4A4A SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr11 60266956 rs4938933 0.887 MS4A4A C C 0.02 1.0202 MS4A4A SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intergenic_region chr11 60266956 rs4938933 0.889 NR C C 0 1 MS4A4A SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology intergenic_region chr11 60266956 rs4938933 1.66E-09 MS4A6A C C 0.88 0.88 MS4A4A SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intergenic_region chr11 60266956 rs4938933 1.73E-09 MS4A6A C C 0.88 0.88 MS4A4A SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intergenic_region chr11 60266956 rs4938933 4.47E-08 MS4A6A C C 0.87 0.87 MS4A4A SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intergenic_region chr11 60266956 rs4938933 5.19E-08 MS4A6A C C 0.88 0.88 MS4A4A SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intergenic_region chr11 60266956 rs4938933 8.20E-12 MS4A6A NR NR 0.89 0.89 MS4A4A SNP-based Disease risk 21460841 Caucasian "ADGC, CHARGE, EADI, GERAD" 48589 All LOAD AD intergenic_region chr11 60292543 rs2044981 0.00000392 MS4A4A NR NR NR NA MS4A4A SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 60312178 rs10792263 3.21E-11 "MS4A4A, MS4A4E" NR NR NR NA MS4A4A SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD downstream_gene_variant chr11 60332956 rs2868121 0.00000192 MS4A6E NR NR NR NA MS4A6E SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr11 60334911 rs2304935 0.000186 MS4A4A G G 0.22 1.24608 MS4A6E SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data MS4A4A brain expression (probe ILMN_2370336) in Temporal cortex (TCX) Expression missense_variant chr11 60334911 rs2304935 0.0111 MS4A4A G G 1.06 1.06 MS4A6E SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD missense_variant chr11 60334911 rs2304935 0.0365 MS4A4A G G 0.09 1.09417 MS4A6E SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data MS4A4A brain expression (probe ILMN_2370336) in Cerebellar tissue (CER) Expression missense_variant chr11 60335034 rs2304933 0.000148 MS4A4A A A 0.22 1.24608 MS4A6E SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data MS4A4A brain expression (probe ILMN_2370336) in Temporal cortex (TCX) Expression missense_variant chr11 60335034 rs2304933 0.0113 MS4A4A A A 1.06 1.06 MS4A6E SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD missense_variant chr11 60335034 rs2304933 0.0365 MS4A4A A A 0.09 1.09417 MS4A6E SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data MS4A4A brain expression (probe ILMN_2370336) in Cerebellar tissue (CER) Expression missense_variant chr11 62566624 rs7124057 1.17E-85 EEF1G NR NR -0.9 0.40657 EEF1G SNP-based eQTL 22685416 Caucasian MAYO 374 All EEF1G expression in Cerebellar Expression intron_variant chr11 62566624 rs7124057 2.78E-44 EEF1G NR NR -1.03 0.357007 EEF1G SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD EEF1G expression in Cerebellar Expression intron_variant chr11 62566624 rs7124057 4.01E-88 EEF1G NR NR -0.7 0.496585 EEF1G SNP-based eQTL 22685416 Caucasian MAYO 399 All EEF1G expression in Temporal cortex Expression intron_variant chr11 62566624 rs7124057 6.83E-36 EEF1G NR NR -0.74 0.477114 EEF1G SNP-based eQTL 22685416 Caucasian MAYO 197 AD EEF1G expression in Cerebellar Expression intron_variant chr11 63837705 rs10792421 0.0000216 MARK2 G G NR NA MARK2 SNP-based Cross phenotype 30930738 Caucasian PGC2-BIP 51710 All Bipolar disorder (BIP) ADRD upstream_gene_variant chr11 63837705 rs10792421 0.0000668 MARK2 G G NR NA MARK2 SNP-based Cross phenotype 30930738 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr11 69200174 rs10896445 0.00031 MYEOV NR NR NR NA AP003071.5 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intergenic_region chr11 69200174 rs10896445 0.0032 MYEOV NR NR NR NA AP003071.5 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intergenic_region chr11 69200174 rs10896445 0.0071 MYEOV NR NR NR NA AP003071.5 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intergenic_region chr11 69200174 rs10896445 0.011 MYEOV NR NR NR NA AP003071.5 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intergenic_region chr11 72354165 rs74766959 0.00032 CLPB NR NR NR NA CLPB SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intron_variant chr11 72354165 rs74766959 0.0008 CLPB NR NR NR NA CLPB SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intron_variant chr11 72354165 rs74766959 0.005 CLPB NR NR NR NA CLPB SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intron_variant chr11 72354165 rs74766959 0.17 CLPB NR NR NR NA CLPB SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intron_variant chr11 74322021 rs3888908 0.00000952 NR A A 1.72 1.72 PGM2L1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr11 76597228 rs11827375 0.0000072 C11orf30 NR NR 1.23 1.23 EMSY SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intergenic_region chr11 76723776 rs1893306 0.0000425 GUCY2EP G G NR NA LRRC32 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr11 76723776 rs1893306 0.00109 GUCY2EP G G 0.95 0.95 LRRC32 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD upstream_gene_variant chr11 76723776 rs1893306 0.00146 GUCY2EP G G NR NA LRRC32 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD upstream_gene_variant chr11 76723776 rs1893306 0.00235 GUCY2EP G G 0.96 0.96 LRRC32 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD upstream_gene_variant chr11 76723776 rs1893306 0.558 GUCY2EP G G 1 1 LRRC32 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD upstream_gene_variant chr11 76723776 rs1893306 0.668 GUCY2EP G G 1.02 1.02 LRRC32 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD upstream_gene_variant chr11 78219453 rs901104 0.000000456 GAP2 C C 3.24 3.24 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78219453 rs901104 0.00000199 GAP2 C C 2.87 2.87 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78219453 rs901104 0.0452 GAP2 C C 2.54 2.54 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78219453 rs901104 0.147 GAP2 C C 2.08 2.08 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78225120 rs1385600 0.000000502 GAP2 T T 3.18 3.18 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD synonymous_variant chr11 78225120 rs1385600 0.0132 GAP2 T T 3 3 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD synonymous_variant chr11 78225120 rs1385600 0.0463 GAP2 T T 5.56 5.56 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD synonymous_variant chr11 78225120 rs1385600 2.81E-09 GAP2 T T 3.65 3.65 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD synonymous_variant chr11 78230030 rs1007837 0.000000397 GAP2 C C 3.01 3.01 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78230030 rs1007837 0.00000478 GAP2 C C 3.18 3.18 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78230030 rs1007837 0.032 GAP2 C C 2.85 2.85 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78230030 rs1007837 0.204 GAP2 C C 1.89 1.89 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78254988 rs2510038 0.0000119 GAP2 C C 2.72 2.72 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78254988 rs2510038 0.0000892 GAP2 C C 2.44 2.44 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78254988 rs2510038 0.0435 GAP2 C C 2.53 2.53 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78254988 rs2510038 0.147 GAP2 C C 2.08 2.08 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78279214 rs4945261 0.000000566 GAP2 G G 3.21 3.21 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78279214 rs4945261 0.042 GAP2 G G 2.54 2.54 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78279214 rs4945261 0.0463 GAP2 G G 5.56 5.56 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78279214 rs4945261 3.06E-08 GAP2 G G 3.44 3.44 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78281921 rs7101429 0.00000106 GAP2 A A 2.96 2.96 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78281921 rs7101429 0.0000462 GAP2 A A 2.13 2.13 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78281921 rs7101429 0.0187 GAP2 A A 2.84 2.84 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78281921 rs7101429 0.0499 GAP2 A A 2.5 2.5 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78285357 rs10793294 0.000000159 GAP2 C C 2.83 2.83 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78285357 rs10793294 0.0000298 GAP2 C C 2.45 2.45 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78285357 rs10793294 0.0134 GAP2 C C 2.66 2.66 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78285357 rs10793294 0.0217 GAP2 C C 4.45 4.45 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78285357 rs10793294 0.025 GAB2 C C 0.82 0.82 GAB2 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr11 78290202 rs4291702 0.000000588 GAP2 C C 2.96 2.96 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78290202 rs4291702 0.00000373 GAP2 C C 3.19 3.19 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78290202 rs4291702 0.0244 GAP2 C C 2.7 2.7 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78290202 rs4291702 0.204 GAP2 C C 1.89 1.89 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78334025 rs7115850 0.00000016 GAP2 C C 3.21 3.21 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78334025 rs7115850 0.00345 GAP2 C C 14.93 14.93 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78334025 rs7115850 0.0391 GAP2 C C 2.48 2.48 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78334025 rs7115850 2.80E-10 GAP2 C C 3.92 3.92 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78380104 rs2373115 0.00000046 GAP2 G G 3.21 3.21 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 360 APOE-e4+ LOAD AD intron_variant chr11 78380104 rs2373115 0.00345 GAP2 G G 14.93 14.93 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 144 APOE-e4+ LOAD AD intron_variant chr11 78380104 rs2373115 0.0391 GAP2 G G 2.48 2.48 GAB2 SNP-based Disease risk 17553421 Caucasian "ADGC, Cohort from Europe" 140 APOE-e4+ LOAD AD intron_variant chr11 78380104 rs2373115 9.66E-11 GAP2 G G 4.06 4.06 GAB2 SNP-based Disease risk 17553421 Caucasian ADGC 644 APOE-e4+ LOAD AD intron_variant chr11 78493334 rs4474465 0.00000341 NARS2 G G 1.44 NA NARS2 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr11 80666008 rs17140547 0.00000796 NR NR NR -532.56 5.15384e-232 TENM4 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intergenic_region chr11 80666008 rs17140547 0.00014 NR T T -711.52 9.79017e-310 TENM4 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intergenic_region chr11 80666008 rs17140547 0.0082 NR T T -409.41 1.56854e-178 TENM4 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr11 80666008 rs17140547 0.039 NR T T NR NA TENM4 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr11 85836460 rs10898417 0.00000117 SYTL2 G G 0.59 0.59 CCDC83 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intergenic_region chr11 85836460 rs10898417 0.003 SYTL2 G G 0.82 0.82 CCDC83 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intergenic_region chr11 85836460 rs10898417 0.83 SYTL2 G G 1.02 1.02 CCDC83 SNP-based Disease risk 23565137 Asian Cohort from Japan 1870 All LOAD AD intergenic_region chr11 85960659 rs618679 0.00000135 PICALM NR NR NR NA PICALM SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 85966428 rs17817600 0.000014 PICALM NR NR NR NA PICALM SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intron_variant chr11 85966428 rs17817600 0.000367 PICALM NR NR 1.41 1.41 PICALM SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD intron_variant chr11 85966428 rs17817600 0.00231 PICALM NR NR 1.36 1.36 PICALM SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD intron_variant chr11 85966428 rs17817600 0.0122 PICALM NR NR 1.38 1.38 PICALM SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD intron_variant chr11 85966428 rs17817600 0.0212 PICALM NR NR 1.25 1.25 PICALM SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD intron_variant chr11 85966428 rs17817600 0.848 PICALM NR NR 0.94 0.94 PICALM SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD intron_variant chr11 85966428 rs17817600 2.17E-08 PICALM NR NR 1.33 1.33 PICALM SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intron_variant chr11 85970540 rs639012 0.000000186 PICALM NR NR 0.86 0.86 PICALM SNP-based Disease risk 30979435 Caucasian ADGC 14880 Age 60-79 y AD AD intron_variant chr11 85970540 rs639012 0.601 PICALM NR NR 0.98 0.98 PICALM SNP-based Disease risk 30979435 Caucasian ADGC 6552 Age >=80 y AD AD intron_variant chr11 85975053 rs532470 0.03 PICALM NR NR 1.12 1.12 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intron_variant chr11 85975053 rs532470 0.048 PICALM G G 1.06 1.06 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr11 85975053 rs532470 0.47 PICALM G G 1.02 1.02 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr11 85975053 rs532470 0.89 PICALM NR NR 0.99 0.99 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intron_variant chr11 85993023 rs12795381 0.0086 PICALM C C 0.49 0.49 PICALM SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr11 86014894 rs592297 0.02 PICALM C C 0.92 0.92 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD synonymous_variant chr11 86014894 rs592297 0.12 PICALM NR NR 0.9 0.9 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD synonymous_variant chr11 86014894 rs592297 0.32 PICALM NR NR 1.04 1.04 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD synonymous_variant chr11 86014894 rs592297 0.33 PICALM C C 0.96 0.96 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD synonymous_variant chr11 86032331 rs10501605 0.112 PICALM G G 0.89 NA PICALM SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr11 86046547 rs677909 0.000033 PICALM C C 0.88 0.88 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr11 86046547 rs677909 0.0062 PICALM NR NR 0.86 0.86 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intron_variant chr11 86046547 rs677909 0.056 PICALM C C 0.94 0.94 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr11 86046547 rs677909 0.8 PICALM NR NR 0.99 0.99 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intron_variant chr11 86046547 rs677909 8.35E-11 PICALM NR NR NR NA PICALM SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 86065502 rs867611 2.19E-18 SUZ12P1 G G -8.75 NA PICALM SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr11 86071625 rs636848 0.27 PICALM NR NR 1.07 1.07 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD upstream_gene_variant chr11 86071625 rs636848 0.44 PICALM NR NR 0.96 0.96 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD upstream_gene_variant chr11 86071625 rs636848 0.6 PICALM G G 1.02 1.02 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD upstream_gene_variant chr11 86071625 rs636848 0.98 PICALM G G 1 1 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD upstream_gene_variant chr11 86075245 rs17159904 0.0424 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86075245 rs17159904 0.0427 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 86075245 rs17159904 0.0495 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86075245 rs17159904 0.653 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 86076782 rs536841 0.011 PICALM NR NR 0.053 1.05443 PICALM SNP-based Endophenotype 21116278 Caucasian "AddNeuroMed, ADNI" 939 All Entorhinal cortex thickness Imaging intergenic_region chr11 86077309 rs541458 0.000026 PICALM C C 0.88 0.88 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intergenic_region chr11 86077309 rs541458 0.0053 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intergenic_region chr11 86077309 rs541458 0.0066 PICALM NR NR 0.86 0.86 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intergenic_region chr11 86077309 rs541458 0.01 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr11 86077309 rs541458 0.01 PICALM C C 0.81 0.81 PICALM SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intergenic_region chr11 86077309 rs541458 0.013 PICALM NR NR 0.052 1.05338 PICALM SNP-based Endophenotype 21116278 Caucasian "AddNeuroMed, ADNI" 939 All Entorhinal cortex thickness Imaging intergenic_region chr11 86077309 rs541458 0.048 PICALM C C 0.94 0.94 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intergenic_region chr11 86077309 rs541458 0.0628 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86077309 rs541458 0.0752 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intergenic_region chr11 86077309 rs541458 0.19 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intergenic_region chr11 86077309 rs541458 0.272 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intergenic_region chr11 86077309 rs541458 0.283 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 86077309 rs541458 0.363 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86077309 rs541458 0.407 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intergenic_region chr11 86077309 rs541458 0.447 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86077309 rs541458 0.515 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intergenic_region chr11 86077309 rs541458 0.54 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr11 86077309 rs541458 0.573 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intergenic_region chr11 86077309 rs541458 0.705 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86077309 rs541458 0.778 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86077309 rs541458 0.794 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 86077309 rs541458 0.81 PICALM NR NR 0.99 0.99 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intergenic_region chr11 86077309 rs541458 0.82 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intergenic_region chr11 86077309 rs541458 0.842 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intergenic_region chr11 86089237 rs561655 0.000000122 PICALM G G 0.88 0.88 PICALM SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD upstream_gene_variant chr11 86089237 rs561655 0.00000046 PICALM G G 0.88 0.88 PICALM SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD upstream_gene_variant chr11 86089237 rs561655 0.000034 PICALM G G 0.89 0.89 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD upstream_gene_variant chr11 86089237 rs561655 0.0000369 PICALM G G 0.86 0.86 PICALM SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD upstream_gene_variant chr11 86089237 rs561655 0.0000844 PICALM G G 0.86 0.86 PICALM SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD upstream_gene_variant chr11 86089237 rs561655 0.0009 PICALM NR NR 0.83 0.83 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD upstream_gene_variant chr11 86089237 rs561655 0.00223 PICALM G G 0.33 1.39097 PICALM SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other upstream_gene_variant chr11 86089237 rs561655 0.0112 PICALM G G 0.32 1.37713 PICALM SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other upstream_gene_variant chr11 86089237 rs561655 0.017 PICALM G G 0.92 0.92 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD upstream_gene_variant chr11 86089237 rs561655 0.117 NR G G -0.05 0.951229 PICALM SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology upstream_gene_variant chr11 86089237 rs561655 0.5 PICALM NR NR 0.97 0.97 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD upstream_gene_variant chr11 86089237 rs561655 1.02E-10 PICALM G G 0.87 0.87 PICALM SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD upstream_gene_variant chr11 86089237 rs561655 7.00E-11 PICALM G G 0.87 0.87 PICALM SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD upstream_gene_variant chr11 86100322 rs526904 0.00501 PICALM NR NR -0.2 NA PICALM SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intergenic_region chr11 86103988 rs1237999 0.009 PICALM NR NR 0.053 1.05443 PICALM SNP-based Endophenotype 21116278 Caucasian "AddNeuroMed, ADNI" 939 All Entorhinal cortex thickness Imaging intergenic_region chr11 86109035 rs543293 0.000023 PICALM A A 0.88 0.88 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intergenic_region chr11 86109035 rs543293 0.0000631 PICALM NR NR 0.3 NA PICALM SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intergenic_region chr11 86109035 rs543293 0.0011 PICALM NR NR 0.83 0.83 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intergenic_region chr11 86109035 rs543293 0.0086 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intergenic_region chr11 86109035 rs543293 0.009 PICALM NR NR 0.054 1.05548 PICALM SNP-based Endophenotype 21116278 Caucasian "AddNeuroMed, ADNI" 939 All Entorhinal cortex thickness Imaging intergenic_region chr11 86109035 rs543293 0.014 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intergenic_region chr11 86109035 rs543293 0.015 PICALM A A 0.92 0.92 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intergenic_region chr11 86109035 rs543293 0.0189 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr11 86109035 rs543293 0.045 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intergenic_region chr11 86109035 rs543293 0.171 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86109035 rs543293 0.272 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 86109035 rs543293 0.349 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intergenic_region chr11 86109035 rs543293 0.367 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intergenic_region chr11 86109035 rs543293 0.406 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 86109035 rs543293 0.517 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr11 86109035 rs543293 0.543 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intergenic_region chr11 86109035 rs543293 0.599 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intergenic_region chr11 86109035 rs543293 0.641 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intergenic_region chr11 86109035 rs543293 0.701 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86109035 rs543293 0.71 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86109035 rs543293 0.722 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86109035 rs543293 0.932 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86109035 rs543293 0.967 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intergenic_region chr11 86109035 rs543293 0.98 PICALM NR NR 1 1 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intergenic_region chr11 86127766 rs10792830 0.0000064 AP003097.1 NR NR 1.25 1.25 PICALM SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intergenic_region chr11 86139201 rs3844143 0.000779 PICALM T T NR NA PICALM SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intergenic_region chr11 86139201 rs3844143 0.162 PICALM T T 0.93 0.93 PICALM SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr11 86139201 rs3844143 1.27E-08 "FNTAL1, LOC100130431" NR NR NR NA PICALM SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr11 86139201 rs3844143 1.33E-16 PICALM T T 0.9 0.9 PICALM SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr11 86139201 rs3844143 1.94E-08 PICALM T T NR NA PICALM SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr11 86139201 rs3844143 5.31E-11 PICALM C C 0.99 0.99 PICALM SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr11 86139201 rs3844143 5.31E-11 PICALM G G NR NA PICALM SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intergenic_region chr11 86139201 rs3844143 6.52E-17 PICALM T T 0.9 0.9 PICALM SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr11 86142965 rs17148827 0.0089 PICALM C C 2.01 2.01 PICALM SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr11 86147496 rs7941541 0.0007 PICALM G G 0.89 0.89 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intergenic_region chr11 86147496 rs7941541 0.019 PICALM NR NR 0.049 1.05022 PICALM SNP-based Endophenotype 21116278 Caucasian "AddNeuroMed, ADNI" 939 All Entorhinal cortex thickness Imaging intergenic_region chr11 86147496 rs7941541 0.0243 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intergenic_region chr11 86147496 rs7941541 0.0338 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intergenic_region chr11 86147496 rs7941541 0.0479 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr11 86147496 rs7941541 0.0596 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intergenic_region chr11 86147496 rs7941541 0.099 PICALM NR NR 0.9 0.9 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intergenic_region chr11 86147496 rs7941541 0.156 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86147496 rs7941541 0.21 PICALM G G 0.95 0.95 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intergenic_region chr11 86147496 rs7941541 0.279 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 86147496 rs7941541 0.39 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 86147496 rs7941541 0.448 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intergenic_region chr11 86147496 rs7941541 0.55 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr11 86147496 rs7941541 0.595 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86147496 rs7941541 0.612 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr11 86147496 rs7941541 0.648 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intergenic_region chr11 86147496 rs7941541 0.684 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intergenic_region chr11 86147496 rs7941541 0.72 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intergenic_region chr11 86147496 rs7941541 0.73 PICALM NR NR 0.98 0.98 PICALM SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intergenic_region chr11 86147496 rs7941541 0.732 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86147496 rs7941541 0.795 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intergenic_region chr11 86147496 rs7941541 0.805 CUGBP2 NR NR NR NA PICALM SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intergenic_region chr11 86147496 rs7941541 0.902 PICALM NR NR NR NA PICALM SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 86148441 rs10898439 2.96E-09 "FNTAL1, LOC100130431" NR NR NR NA PICALM SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr11 86156833 rs10792832 0.00013 PICALM A A 0.8 0.8 PICALM SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology downstream_gene_variant chr11 86156833 rs10792832 0.00021 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in medulla (MEDU) Expression downstream_gene_variant chr11 86156833 rs10792832 0.0017 PICALM A A 0.79 0.79 PICALM SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology downstream_gene_variant chr11 86156833 rs10792832 0.0041 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in putamen (PUTM) Expression downstream_gene_variant chr11 86156833 rs10792832 0.0044 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in thalamus (THAL) Expression downstream_gene_variant chr11 86156833 rs10792832 0.12 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in intra-locular white matter (WHMT) Expression downstream_gene_variant chr11 86156833 rs10792832 0.12 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in substantia nigra (SNIG) Expression downstream_gene_variant chr11 86156833 rs10792832 0.22 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in temporal cortex (TCTX) Expression downstream_gene_variant chr11 86156833 rs10792832 0.36 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in occipital cortex (OCTX) Expression downstream_gene_variant chr11 86156833 rs10792832 0.44 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in cerebellar cortex (CRBL) Expression downstream_gene_variant chr11 86156833 rs10792832 0.56 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in hippocampus (HIPP) Expression downstream_gene_variant chr11 86156833 rs10792832 0.98 EED NR NR NR NA PICALM SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects EED (t3343202) expression in frontal cortex (FCTX) Expression downstream_gene_variant chr11 86156833 rs10792832 1.10E-11 PICALM A A 0.85 0.85 PICALM SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD downstream_gene_variant chr11 86156833 rs10792832 1.12E-17 PICALM G G NR NA PICALM SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD downstream_gene_variant chr11 86156833 rs10792832 6.50E-16 PICALM A A 0.88 0.88 PICALM SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD downstream_gene_variant chr11 86156833 rs10792832 9.30E-26 PICALM A A 0.87 0.87 PICALM SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD downstream_gene_variant chr11 86156833 rs10792832 NR PICALM G G 1.16 1.16 PICALM SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD downstream_gene_variant chr11 86156833 rs10792832 NR ZCWPW1 G G 1.03 1.03 PICALM SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD downstream_gene_variant chr11 86156833 rs10792832 NR ZCWPW1 G G 1.15 1.15 PICALM SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD downstream_gene_variant chr11 86157598 rs3851179 0.000000019 PICALM NR NR 0.85 0.85 EED SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.00000281 PICALM T T 0.89 0.89 EED SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.0000122 PICALM T T 0.86 0.86 EED SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.0000171 PICALM T T 0.8 0.8 EED SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.000039 PICALM T T 0.89 0.89 EED SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.0034 PICALM NR NR 0.86 0.86 EED SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD downstream_gene_variant chr11 86157598 rs3851179 0.006 PICALM A A 0.87 0.87 EED SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.007 PICALM NR NR 0.84 0.84 EED SNP-based Disease risk 20460622 Caucasian Cohort from Europe 2349 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.01 PICALM NR NR 0.066 1.06823 EED SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Entorhinal cortex thickness Imaging downstream_gene_variant chr11 86157598 rs3851179 0.014 PICALM NR NR 0.9 0.9 EED SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 4363 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.0152 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.018 PICALM A A 0.84 0.84 EED SNP-based Disease risk 21390209 Caucasian ADGC 1525 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.0199 PICALM T T 0.79 0.79 EED SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.021 PICALM NR NR NR NA EED SNP-based Endophenotype 21390209 Caucasian "ADNI, leadC" 597 AD subjects AD Progression Cognitive downstream_gene_variant chr11 86157598 rs3851179 0.026 PICALM T T 0.93 0.93 EED SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.034 PICALM NR NR 0.043 1.04394 EED SNP-based Endophenotype 21116278 Caucasian "AddNeuroMed, ADNI" 939 All Entorhinal cortex thickness Imaging downstream_gene_variant chr11 86157598 rs3851179 0.039 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.04 PICALM NR NR 0.061 1.0629 EED SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Hippocampal volume Imaging downstream_gene_variant chr11 86157598 rs3851179 0.06 PICALM NR NR 0.033 1.03355 EED SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Temporal pole cortex thickness Imaging downstream_gene_variant chr11 86157598 rs3851179 0.0817 PICALM NR NR NR NA EED SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.118 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.118 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.157 PICALM T T 0.85 0.85 EED SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.171 PICALM A A 0.9 0.9 EED SNP-based Disease risk 21390209 Caucasian GenADA 1574 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.199 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.21 PICALM NR NR NR NA EED SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.29 PICALM NR NR 0.014 1.0141 EED SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Parahippocampal gyrus cortex thickness Imaging downstream_gene_variant chr11 86157598 rs3851179 0.321 PICALM NR NR NR NA EED SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.39 PICALM NR NR 0.94 0.94 EED SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging downstream_gene_variant chr11 86157598 rs3851179 0.392 PICALM A A 0.89 0.89 EED SNP-based Disease risk 21390209 Caucasian ADNI 496 All AD AD downstream_gene_variant chr11 86157598 rs3851179 0.446 PICALM NR NR NR NA EED SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.47 PICALM NR NR 0.009 1.00904 EED SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Amygdala volume Imaging downstream_gene_variant chr11 86157598 rs3851179 0.629 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.632 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.653 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.655 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.677 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.695 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.73 PICALM NR NR 0.99 0.99 EED SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD downstream_gene_variant chr11 86157598 rs3851179 0.799 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.851 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD downstream_gene_variant chr11 86157598 rs3851179 0.87 PICALM NR NR 0.99 0.99 EED SNP-based Disease risk 20558387 Caucasian ADNI 740 All AD + MCI AD downstream_gene_variant chr11 86157598 rs3851179 0.97 PICALM NR NR -0.005 0.995012 EED SNP-based Endophenotype 20558387 Caucasian ADNI 740 All White matter lesion volume Imaging downstream_gene_variant chr11 86157598 rs3851179 0.976 CUGBP2 NR NR NR NA EED SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD downstream_gene_variant chr11 86157598 rs3851179 1.30E-09 PICALM NR NR 0.86 0.86 EED SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 19052 All AD AD downstream_gene_variant chr11 86157598 rs3851179 3.16E-12 PICALM T T 0.87 0.87 EED SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD downstream_gene_variant chr11 86157598 rs3851179 5.80E-16 PICALM T T 0.89 0.89 EED SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD downstream_gene_variant chr11 86157598 rs3851179 6.00E-25 PICALM T T 0.88 0.88 EED SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD downstream_gene_variant chr11 86157598 rs3851179 6.10E-11 PICALM T T 0.85 0.85 EED SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD downstream_gene_variant chr11 93036582 rs271057 0.0000068 "MTNR1B, SLC36A4" NR NR NR NA MTNR1B SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr11 94963977 rs7937776 0.0006 HSPC148 C C NR NA CWC15 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr11 94963977 rs7937776 0.00067 HSPC148 C C NR NA CWC15 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr11 94963977 rs7937776 0.0007 HSPC148 C C NR NA CWC15 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr11 95804194 rs3017756 0.0113 CEP57 NR NR NR NA CEP57 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr11 97180604 rs1690600 0.00000162 NR NR NR NR NA JRKL SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr11 97180784 rs1793382 0.00000128 NR NR NR NR NA JRKL SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr11 98646026 rs3018573 0.00000681 NR G G NR NA CNTN5 SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intergenic_region chr11 99206206 rs10892901 0.0196 CNTN5 NR NR NR NA CNTN5 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr11 99886997 rs10501927 0.000002 CNTN5 NR NR 1.18 1.18 CNTN5 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr11 99886997 rs10501927 0.002 CNTN5 NR NR 0.119 1.12637 CNTN5 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All White matter lesion volume Imaging intron_variant chr11 99886997 rs10501927 0.02 CNTN5 NR NR -0.067 0.935195 CNTN5 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Entorhinal cortex thickness Imaging intron_variant chr11 99886997 rs10501927 0.02 CR1 NR NR -0.051 0.950279 CNTN5 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Temporal pole cortex thickness Imaging intron_variant chr11 99886997 rs10501927 0.03 CNTN5 NR NR 1.25 1.25 CNTN5 SNP-based Disease risk 20558387 Caucasian ADNI 740 All AD + MCI AD intron_variant chr11 99886997 rs10501927 0.05 CNTN5 NR NR -0.04 0.960789 CNTN5 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Parahippocampal gyrus cortex thickness Imaging intron_variant chr11 99886997 rs10501927 0.17 CNTN5 NR NR -0.046 0.955042 CNTN5 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Hippocampal volume Imaging intron_variant chr11 99886997 rs10501927 0.19 CNTN5 NR NR -0.018 0.982161 CNTN5 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Amygdala volume Imaging intron_variant chr11 102809498 rs603050 0.000000178 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker intron_variant chr11 102809498 rs603050 0.00000439 MMP3 T T NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker intron_variant chr11 102809498 rs603050 0.0000986 MMP3 T T NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker intron_variant chr11 102809498 rs603050 0.000118 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102809498 rs603050 0.00369 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102809498 rs603050 0.00395 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker intron_variant chr11 102809498 rs603050 0.268 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker intron_variant chr11 102809498 rs603050 0.4 MMP3 NR NR 0.015 1.01511 MMP1 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr11 102809498 rs603050 0.67 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr11 102809498 rs603050 0.75 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr11 102809498 rs603050 0.9 MMP3 NR NR NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr11 102809498 rs603050 1.84E-09 MMP3 T T NR NA MMP1 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 0.000032 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 0.0000612 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 0.0292 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 0.091 MMP3 NR NR -0.027 0.973361 MMP3 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr11 102820751 rs11225434 0.86 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr11 102820751 rs11225434 0.91 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr11 102820751 rs11225434 0.94 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr11 102820751 rs11225434 1.69E-12 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 4.50E-39 MMP3 C C NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 4.94E-24 MMP3 C C NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 5.67E-14 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker intron_variant chr11 102820751 rs11225434 7.38E-17 MMP3 C C NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 0.000000232 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 0.00000184 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 0.00000773 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 0.00025 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 0.00607 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 0.29 MMP3 NR NR 0.018 1.01816 MMP3 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr11 102824377 rs495366 0.466 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 0.64 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr11 102824377 rs495366 0.78 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr11 102824377 rs495366 0.92 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr11 102824377 rs495366 2.25E-09 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102824377 rs495366 6.19E-11 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 0.000000122 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 0.000000152 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 0.0489 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 0.053 MMP3 NR NR -0.029 0.971416 MMP3 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr11 102827993 rs7926920 0.74 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr11 102827993 rs7926920 0.76 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr11 102827993 rs7926920 0.99 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr11 102827993 rs7926920 1.32E-25 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 1.57E-18 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 1.90E-13 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 1.95E-14 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker intron_variant chr11 102827993 rs7926920 2.56E-42 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 0.000000177 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 0.000000829 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 0.0000268 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 0.000266 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 0.00346 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 0.31 MMP3 NR NR 0.018 1.01816 MMP3 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr11 102838056 rs650108 0.562 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 0.59 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr11 102838056 rs650108 0.63 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr11 102838056 rs650108 0.95 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr11 102838056 rs650108 1.01E-10 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker intron_variant chr11 102838056 rs650108 1.33E-08 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker intron_variant chr11 102842889 rs679620 0.0444 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker missense_variant chr11 102842889 rs679620 0.046 MMP3 NR NR -0.032 0.968507 MMP3 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD missense_variant chr11 102842889 rs679620 0.51 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker missense_variant chr11 102842889 rs679620 0.68 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker missense_variant chr11 102842889 rs679620 0.96 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker missense_variant chr11 102842889 rs679620 1.54E-09 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker missense_variant chr11 102842889 rs679620 3.07E-14 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker missense_variant chr11 102842889 rs679620 4.93E-44 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker missense_variant chr11 102842889 rs679620 6.05E-15 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker missense_variant chr11 102842889 rs679620 6.36E-26 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker missense_variant chr11 102842889 rs679620 7.12E-20 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker missense_variant chr11 102842889 rs679620 9.95E-08 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker missense_variant chr11 102845590 rs645419 0.039 MMP3 NR NR -0.032 0.968507 MMP3 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr11 102845590 rs645419 0.0444 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 0.5 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 0.68 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 0.96 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 1.02E-09 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 3.07E-14 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 3.26E-44 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 4.10E-15 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 4.15E-26 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 7.12E-20 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102845590 rs645419 9.95E-08 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 0.038 MMP3 NR NR -0.032 0.968507 MMP3 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr11 102846249 rs573521 0.0444 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 0.5 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 0.67 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 0.812 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 0.93 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 2.39E-44 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 3.00E-26 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 3.07E-14 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 3.40E-15 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 7.12E-20 MMP3 A A NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102846249 rs573521 9.95E-08 MMP3 NR NR NR NA MMP3 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker upstream_gene_variant chr11 102862432 rs12808148 0.00000124 "MMP3, MMP12" NR NR 0.81 0.81 MMP12 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD downstream_gene_variant chr11 102862432 rs12808148 0.0000102 "MMP3, MMP12" NR NR NR NA MMP12 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD downstream_gene_variant chr11 102862432 rs12808148 0.00138 "MMP3, MMP12" NR NR 0.76 0.76 MMP12 SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD downstream_gene_variant chr11 102862432 rs12808148 0.015 "MMP3, MMP12" NR NR 0.82 0.82 MMP12 SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD downstream_gene_variant chr11 102862432 rs12808148 0.0455 "MMP3, MMP12" NR NR 0.82 0.82 MMP12 SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD downstream_gene_variant chr11 102862432 rs12808148 0.056 "MMP3, MMP12" NR NR 0.62 0.62 MMP12 SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD downstream_gene_variant chr11 102862432 rs12808148 0.139 "MMP3, MMP12" NR NR 0.87 0.87 MMP12 SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD downstream_gene_variant chr11 102900410 rs948399 0.000000178 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF MMP3 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.000000542 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF MMP3 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.000000961 MMP3 T T NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF MMP3 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.00000893 MMP3 T T NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF MMP3 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.0000228 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF MMP3 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.0000635 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF MMP3 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.0137 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma MMP3 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.18 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.23 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 0.74 MMP3 NR NR 0.006 1.00602 MMP12 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD downstream_gene_variant chr11 102900410 rs948399 0.76 MMP3 NR NR NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker downstream_gene_variant chr11 102900410 rs948399 4.29E-11 MMP3 T T NR NA MMP12 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF MMP3 Fluid biomarker downstream_gene_variant chr11 105974196 rs509512 0.00000737 GRIA4 C C 0.75 0.75 GRIA4 SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD intron_variant chr11 105974196 rs509512 0.133 GRIA4 C C 0.94 0.94 GRIA4 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD intron_variant chr11 105974196 rs509512 0.439 GRIA4 C C 1.04 1.04 GRIA4 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD intron_variant chr11 111017760 rs978769 0.0000029 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 111017760 rs978769 0.000074 NR NR NR 0.66 0.66 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 111017760 rs978769 0.000287 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 111017760 rs978769 0.00308 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 111017760 rs978769 0.00681 NR NR NR 0.56 0.56 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 111017760 rs978769 0.0572 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr11 111017760 rs978769 0.0605 NR NR NR 0.73 0.73 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 111017760 rs978769 0.25093 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr11 111017760 rs978769 0.674 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intergenic_region chr11 111017868 rs978770 0.00000149 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 111017868 rs978770 0.000041 NR NR NR 0.65 0.65 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 111017868 rs978770 0.000223 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 111017868 rs978770 0.00208 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 111017868 rs978770 0.00527 NR NR NR 0.56 0.56 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 111017868 rs978770 0.0406 NR NR NR 0.72 0.72 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 111017868 rs978770 0.05678 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr11 111017868 rs978770 0.25242 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr11 111017868 rs978770 0.683 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intergenic_region chr11 111019216 rs11213703 0.00000235 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 111019216 rs11213703 0.000063 NR NR NR 0.66 0.66 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr11 111019216 rs11213703 0.000287 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 111019216 rs11213703 0.00246 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 111019216 rs11213703 0.00681 NR NR NR 0.56 0.56 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr11 111019216 rs11213703 0.0534 NR NR NR 0.72 0.72 C11orf53 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr11 111019216 rs11213703 0.06128 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr11 111019216 rs11213703 0.30704 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr11 111019216 rs11213703 0.633 NR NR NR NR NA C11orf53 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intergenic_region chr11 116807007 rs1263167 0.0342 APOA4 NR NR -4.36 0.0127784 APOA4 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma ApoA-IV Fluid biomarker intergenic_region chr11 116807007 rs1263167 6.84E-31 APOA4 NR NR -0.15 0.860708 APOA4 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma ApoA-IV Fluid biomarker intergenic_region chr11 116807697 rs1263170 0.000655 APOA4 T T NR NA APOA4 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr11 116807697 rs1263170 0.00337 APOA4 T T 1.05 1.05 APOA4 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr11 116807697 rs1263170 0.00422 APOA4 T T 1.04 1.04 APOA4 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr11 116807697 rs1263170 0.442 APOA4 T T 1 1 APOA4 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr11 116807697 rs1263170 0.895 APOA4 T T 1.01 1.01 APOA4 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr11 116807697 rs1263170 4.33E-09 APOA4 T T NR NA APOA4 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total triglycerides (TG) Non-ADRD intergenic_region chr11 118559804 rs11552421 1.55E-147 TMEM25 NR NR 2.67 14.44 IFT46 SNP-based eQTL 22685416 Caucasian MAYO 374 All TMEM25 expression in Cerebellar Expression missense_variant chr11 118559804 rs11552421 6.37E-63 TMEM25 NR NR 2.69 14.7317 IFT46 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD TMEM25 expression in Cerebellar Expression missense_variant chr11 118559804 rs11552421 7.41E-77 TMEM25 NR NR 2.65 14.154 IFT46 SNP-based eQTL 22685416 Caucasian MAYO 197 AD TMEM25 expression in Cerebellar Expression missense_variant chr11 121451045 rs4935774 0.809 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121453498 rs17125349 0.236 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121458245 rs661057 0.01 SORL1 C C 0.94 0.94 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 16753 All AD AD intron_variant chr11 121458245 rs661057 0.31 SORL1 C C 0.97 0.97 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 12813 All AD AD intron_variant chr11 121458245 rs661057 0.61 SORL1 C C 1.05 1.05 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 888 All AD AD intron_variant chr11 121458687 rs610188 0.415 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121467284 rs1784934 0.513 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121469524 rs676160 0.399 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121478402 rs11218304 0.01 SORL1 C C 1.1 1.1 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 5924 All AD AD intron_variant chr11 121478402 rs11218304 0.06 SORL1 C C 1.13 1.13 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 1984 All AD AD intron_variant chr11 121488556 rs676759 0.648 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121490175 rs560573 0.119 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121490306 rs2298525 0.883 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121491607 rs985421 0.343 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121496917 rs12364988 0.352 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD synonymous_variant chr11 121497212 rs668387 0.001 SORL1 C C 1.08 1.08 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 20742 All AD AD intron_variant chr11 121497212 rs668387 0.01 SORL1 C C 1.07 1.07 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 16802 All AD AD intron_variant chr11 121497212 rs668387 0.523 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121497212 rs668387 0.99 SORL1 C C 0.99 0.99 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 1753 All AD AD intron_variant chr11 121498541 rs2101756 0.0192 SORL1 C C 1.19 1.19 SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121500411 rs689021 0.007 SORL1 G G 1.06 1.06 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 26308 All AD AD intron_variant chr11 121500411 rs689021 0.03 SORL1 G G 1.05 1.05 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 22368 All AD AD intron_variant chr11 121500411 rs689021 0.82 SORL1 G G 0.99 0.99 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 1753 All AD AD intron_variant chr11 121505242 rs4598682 0.0000095 SORL1 G G 0.75 0.75 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intron_variant chr11 121505242 rs4598682 0.0000225 SORL1 G G 0.68 0.68 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr11 121505242 rs4598682 0.0036 SORL1 G G 0.82 0.82 SORL1 SNP-based Disease risk 23565137 Multi-ethnic "ADGC, Cohorts from Japan and Korea " 30559 All LOAD AD intron_variant chr11 121505242 rs4598682 0.05 SORL1 G G 0.83 0.83 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Japan 1870 All LOAD AD intron_variant chr11 121505242 rs4598682 0.68 SORL1 G G 1.04 1.04 SORL1 SNP-based Disease risk 23565137 Caucasian ADGC 22771 All LOAD AD intron_variant chr11 121510256 rs641120 0.002 SORL1 C C 1.08 1.08 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 15812 All AD AD intron_variant chr11 121510256 rs641120 0.006 SORL1 C C 1.08 1.08 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 15411 All AD AD intron_variant chr11 121510256 rs641120 0.42 SORL1 C C 0.92 0.92 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 865 All AD AD intron_variant chr11 121512162 rs11218313 0.0203 SORL1 C C 1.55 1.55 SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121522517 rs12285364 0.006 SORL1 C C 0.8 0.8 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 6694 All AD AD intron_variant chr11 121522517 rs12285364 0.03 SORL1 C C 0.75 0.75 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 2754 All AD AD intron_variant chr11 121522517 rs12285364 0.07 SORL1 C C 0.82 0.82 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 888 All AD AD intron_variant chr11 121522517 rs12285364 0.662 SORL1 T T 1.09 1.09 SORL1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr11 121533842 rs17125423 0.338 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121538247 rs626885 0.0362 SORL1 T T 1.19 1.19 SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121543767 rs2276346 0.0933 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121544603 rs10502262 0.106 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121552931 rs7946599 0.00000966 SORL1 A A 0.4545 1.57539 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121552931 rs7946599 0.00858 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121552931 rs7946599 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121552931 rs7946599 0.0491 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121554173 rs2298814 0.00000376 SORL1 A A 0.4234 1.52715 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121554173 rs2298814 0.00858 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121554173 rs2298814 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121554173 rs2298814 0.0491 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121555333 rs6589885 0.00000257 SORL1 A A 0.4004 1.49242 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121555333 rs6589885 0.00858 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121555333 rs6589885 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121555333 rs6589885 0.0491 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121556161 rs7131432 0.00000275 SORL1 A A 0.3804 1.46287 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121556161 rs7131432 0.0387 SORL1 A A 1.73 1.73 SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121556550 rs1790208 0.348 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121560645 rs11218340 0.608 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121563084 rs720099 0.00000251 SORL1 T T 0.36 1.43333 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121563084 rs720099 0.00851 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121563084 rs720099 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121563084 rs720099 0.0486 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121563719 rs11218342 0.0000026 SORL1 T T 0.36 1.43333 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121563719 rs11218342 0.00851 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121563719 rs11218342 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121563719 rs11218342 0.0486 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121563847 rs10892756 0.73 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121564878 rs11218343 0.000000027 SORL1 C C 0.81 0.81 SORL1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr11 121564878 rs11218343 0.0000001 SORL1 C C 0.75 0.75 SORL1 SNP-based Disease risk 23565137 Caucasian ADGC 22771 All LOAD AD intron_variant chr11 121564878 rs11218343 0.00000272 SORL1 T T 0.35 1.41907 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121564878 rs11218343 0.00000281 SORL1 C C NR NA SORL1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr11 121564878 rs11218343 0.000018 SORL1 C C 0.77 0.77 SORL1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr11 121564878 rs11218343 0.00004 SORL1 C C 0.78 0.78 SORL1 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr11 121564878 rs11218343 0.00038 SORL1 C C 0.83 0.83 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intron_variant chr11 121564878 rs11218343 0.00158 SORL1 NR NR 0.18 NA SORL1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr11 121564878 rs11218343 0.0043 SORL1 C C 0.68 0.68 SORL1 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr11 121564878 rs11218343 0.00851 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121564878 rs11218343 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121564878 rs11218343 0.0486 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121564878 rs11218343 0.1 SORL1 C C 0.74 0.74 SORL1 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr11 121564878 rs11218343 0.233 SORL1 C C 0.864 0.864 SORL1 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr11 121564878 rs11218343 0.57 SORL1 NR NR 0.81 0.81 SORL1 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr11 121564878 rs11218343 0.636 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121564878 rs11218343 0.68 SORL1 C C 0.96 0.96 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr11 121564878 rs11218343 1.09E-11 SORL1 C C -6.79 NA SORL1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr11 121564878 rs11218343 2.20E-09 SORL1 C C 0.81 0.81 SORL1 SNP-based Disease risk 23565137 Multi-ethnic "ADGC, Cohorts from Japan and Korea " 28133 All LOAD AD intron_variant chr11 121564878 rs11218343 2.90E-12 SORL1 C C 0.8 0.8 SORL1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr11 121564878 rs11218343 5.00E-11 SORL1 C C 0.76 0.76 SORL1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr11 121564878 rs11218343 5.57E-11 SORL1 C C NR NA SORL1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr11 121564878 rs11218343 9.70E-15 SORL1 C C 0.77 0.77 SORL1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr11 121564878 rs11218343 NR SORL1 T T 1.72 1.72 SORL1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr11 121564878 rs11218343 NR ZCWPW1 T T 1.45 1.45 SORL1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr11 121564878 rs11218343 NR ZCWPW1 T T 2.99 2.99 SORL1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr11 121568472 rs11218346 0.466 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121568956 rs1784919 0.00000188 SORL1 T T 0.3586 1.43132 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121568956 rs1784919 0.00843 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121568956 rs1784919 0.0481 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121568956 rs1784919 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121570811 rs1792124 0.00000183 SORL1 A A 0.359 1.4319 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121570811 rs1792124 0.00843 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121570811 rs1792124 0.0481 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121570811 rs1792124 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121570811 rs1792124 0.615 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121571480 rs1790213 0.295 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121575231 rs3781834 0.00000073 SORL1 G G 0.74 0.74 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intron_variant chr11 121575231 rs3781834 0.00079 SORL1 G G 0.78 0.78 SORL1 SNP-based Disease risk 23565137 Caucasian ADGC 22771 All LOAD AD intron_variant chr11 121575231 rs3781834 0.55 SORL1 G G 0.94 0.94 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr11 121575231 rs3781834 9.90E-09 SORL1 G G 0.78 0.78 SORL1 SNP-based Disease risk 23565137 Multi-ethnic "ADGC, Cohorts from Japan and Korea " 28133 All LOAD AD intron_variant chr11 121575839 rs11218347 0.782 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121577381 rs2070045 0.001 SORL1 G G 1.27 1.27 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 1443 All AD AD synonymous_variant chr11 121577381 rs2070045 0.02 SORL1 G G 1.08 1.08 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 19206 All AD AD synonymous_variant chr11 121577381 rs2070045 0.1 SORL1 G G 1.05 1.05 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 15266 All AD AD synonymous_variant chr11 121577545 rs3781835 0.000000316 S0RL1 NR NR NR NA SORL1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr11 121577545 rs3781835 0.00000314 SORL1 A A 0.3501 1.41921 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121577545 rs3781835 0.00624 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121577545 rs3781835 0.0346 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121577545 rs3781835 0.0483 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121581217 rs1699103 0.86 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121581231 rs7116734 0.102 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121581325 rs1792127 0.157 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121581942 rs11218350 0.787 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121582808 rs3781838 0.00000329 SORL1 T T 0.35 1.41907 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121582808 rs3781838 0.00406 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr11 121582808 rs3781838 0.0307 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr11 121582808 rs3781838 0.0331 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr11 121586253 rs1699102 0.07 SORL1 C C 0.78 0.78 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 865 All AD AD synonymous_variant chr11 121586253 rs1699102 0.21 SORL1 C C 1.03 1.03 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 20850 All AD AD synonymous_variant chr11 121586253 rs1699102 0.54 SORL1 C C 1.02 1.02 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 16910 All AD AD synonymous_variant chr11 121589615 rs12272618 0.00000274 SORL1 T T 0.35 1.41907 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121590137 rs2276412 0.000000468 SORL1 NR NR NR NA SORL1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD synonymous_variant chr11 121590137 rs2276412 0.00000264 SORL1 T T 0.3531 1.42347 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD synonymous_variant chr11 121593379 rs10892759 0.112 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121597547 rs7939826 0.00000269 SORL1 T T 0.3463 1.41383 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121602682 rs11218360 0.936 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121602889 rs7128608 0.946 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121603530 rs17125523 0.0000033 SORL1 G G 0.82 0.82 SORL1 SNP-based Disease risk 23565137 Multi-ethnic "ADGC, Cohorts from Japan and Korea " 28133 All LOAD AD intron_variant chr11 121603530 rs17125523 0.0000055 SORL1 G G 0.77 0.77 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intron_variant chr11 121603530 rs17125523 0.034 SORL1 G G 0.85 0.85 SORL1 SNP-based Disease risk 23565137 Caucasian ADGC 22771 All LOAD AD intron_variant chr11 121603530 rs17125523 0.72 SORL1 G G 0.96 0.96 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr11 121605213 rs3824968 0.62 SORL1 T T 0.99 0.99 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 16307 All AD AD synonymous_variant chr11 121605213 rs3824968 0.62 SORL1 T T 1.02 1.02 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 20247 All AD AD synonymous_variant chr11 121605213 rs3824968 <0.001 SORL1 T T 0.79 0.79 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 1753 All AD AD synonymous_variant chr11 121606387 rs1629493 0.266 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121607107 rs3737529 0.0000041 SORL1 T T 0.77 0.77 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intron_variant chr11 121607107 rs3737529 0.0000051 SORL1 T T 0.82 0.82 SORL1 SNP-based Disease risk 23565137 Multi-ethnic "ADGC, Cohorts from Japan and Korea " 28133 All LOAD AD intron_variant chr11 121607107 rs3737529 0.016 SORL1 T T 0.83 0.83 SORL1 SNP-based Disease risk 23565137 Caucasian ADGC 22771 All LOAD AD intron_variant chr11 121607107 rs3737529 0.7 SORL1 T T 1.04 1.04 SORL1 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr11 121607786 rs2282648 0.202 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121608249 rs2282649 0.22 SORL1 C C 0.96 0.96 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 19195 All AD AD intron_variant chr11 121608249 rs2282649 0.69 SORL1 C C 0.99 0.99 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 15255 All AD AD intron_variant chr11 121608249 rs2282649 0.97 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121608249 rs2282649 <0.001 SORL1 C C 0.76 0.76 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 1753 All AD AD intron_variant chr11 121610698 rs726601 0.19 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121612229 rs1784931 0.138 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121612692 rs1010159 0.02 SORL1 C C 1.21 1.21 SORL1 SNP-based Disease risk 21220680 Asian "Cohorts from Asia, Europe, and USA" 1198 All AD AD intron_variant chr11 121612692 rs1010159 0.255 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121612692 rs1010159 0.47 SORL1 C C 0.98 0.98 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 12180 All AD AD intron_variant chr11 121612692 rs1010159 0.62 SORL1 C C 1.01 1.01 SORL1 SNP-based Disease risk 21220680 Caucasian "Cohorts from Asia, Europe, and USA" 16120 All AD AD intron_variant chr11 121616105 rs1503413 0.569 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121618707 rs1784933 0.000363 SORL1 A A 0.22 1.24608 SORL1 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr11 121618707 rs1784933 0.0367 SORL1 A A 1.34 NA SORL1 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr11 121622292 rs1614735 0.435 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121623318 rs17125558 0.793 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121623380 rs17125561 0.462 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 121627175 rs10892761 0.466 SORL1 NR NR NR NA SORL1 SNP-based Disease risk 17975299 Caucasian "ADGC, Cohorts from Europe and USA" 1086 All AD AD intron_variant chr11 124736389 rs12807809 0.18 NRGN NR NR 0.88 0.88 NRGN SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD upstream_gene_variant chr11 124736389 rs12807809 0.83 NRGN NR NR 0.99 0.99 NRGN SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD upstream_gene_variant chr11 125323700 rs11601321 0.00000803 PKNOX2 G G 1.63 NA PKNOX2 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr11 129964624 rs55746218 0.00933 PRDM10 C C NR NA PRDM10 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr11 129964624 rs55746218 2.10E-09 NR C C NR NA PRDM10 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) PRDM10 expression in Cerebellar hemisphere Expression intron_variant chr11 130118110 rs12269733 0.000537 ST14 G G NR NA APLP2 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr11 130118110 rs12269733 1.27E-17 NR G G NR NA APLP2 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group ST14 (ILMN_1699887) expression Expression intron_variant chr11 130165703 rs34008994 0.000155 ST14 C C NR NA ST14 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr11 130165703 rs34008994 2.79E-08 NR C C NR NA ST14 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group ST14 (ENSG00000149418) expression Expression intron_variant chr11 132065380 rs1629316 0.000000008 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intron_variant chr11 132065380 rs1629316 0.0007 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intron_variant chr11 132065380 rs1629316 0.05 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intron_variant chr11 132065380 rs1629316 0.07 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intron_variant chr11 132065380 rs1629316 0.1 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intron_variant chr11 132065380 rs1629316 0.21 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intron_variant chr11 132065380 rs1629316 0.35 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intron_variant chr11 132065380 rs1629316 0.41 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intron_variant chr11 132065380 rs1629316 0.94 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intron_variant chr11 132076884 rs1547897 0.0006 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intron_variant chr11 132076884 rs1547897 0.05 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intron_variant chr11 132076884 rs1547897 0.06 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intron_variant chr11 132076884 rs1547897 0.16 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intron_variant chr11 132076884 rs1547897 0.16 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intron_variant chr11 132076884 rs1547897 0.29 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intron_variant chr11 132076884 rs1547897 0.39 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intron_variant chr11 132076884 rs1547897 1 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intron_variant chr11 132076884 rs1547897 4.80E-09 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intron_variant chr11 132108262 rs11222931 0.0007 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intron_variant chr11 132108262 rs11222931 0.05 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intron_variant chr11 132108262 rs11222931 0.07 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intron_variant chr11 132108262 rs11222931 0.15 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intron_variant chr11 132108262 rs11222931 0.16 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intron_variant chr11 132108262 rs11222931 0.27 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intron_variant chr11 132108262 rs11222931 0.33 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intron_variant chr11 132108262 rs11222931 0.87 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intron_variant chr11 132108262 rs11222931 4.50E-09 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intron_variant chr11 132108367 rs11222932 0.0006 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intron_variant chr11 132108367 rs11222932 0.05 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intron_variant chr11 132108367 rs11222932 0.07 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intron_variant chr11 132108367 rs11222932 0.15 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intron_variant chr11 132108367 rs11222932 0.18 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intron_variant chr11 132108367 rs11222932 0.3 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intron_variant chr11 132108367 rs11222932 0.34 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intron_variant chr11 132108367 rs11222932 0.86 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intron_variant chr11 132108367 rs11222932 4.60E-09 HNT NA NA NA NA NTM SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intron_variant chr11 132823315 rs11223225 0.0004 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intron_variant chr11 132823315 rs11223225 0.02 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intron_variant chr11 132823315 rs11223225 0.03 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intron_variant chr11 132823315 rs11223225 0.06 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intron_variant chr11 132823315 rs11223225 0.09 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intron_variant chr11 132823315 rs11223225 0.26 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intron_variant chr11 132823315 rs11223225 0.26 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intron_variant chr11 132823315 rs11223225 0.47 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intron_variant chr11 132823315 rs11223225 3.20E-11 OPCML NA NA NA NA OPCML SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intron_variant chr12 2236129 rs1006737 0.53 CACNA1C NR NR 1.05 1.05 CACNA1C SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr12 2236129 rs1006737 0.89 CACNA1C NR NR 1.01 1.01 CACNA1C SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr12 5658219 rs4930776 0.0000032 ANO2 NR NR NR NA ANO2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intron_variant chr12 11052141 rs2708389 1.24E-106 TAS2R43 NR NR 1.07 2.91538 PRH1 SNP-based eQTL 22685416 Caucasian MAYO 374 All TAS2R43 expression in Cerebellar Expression intron_variant chr12 11052141 rs2708389 2.34E-47 TAS2R43 NR NR 1.01 2.7456 PRH1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD TAS2R43 expression in Cerebellar Expression intron_variant chr12 11052141 rs2708389 4.12E-53 TAS2R43 NR NR 1.13 3.09566 PRH1 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD TAS2R43 expression in Cerebellar Expression intron_variant chr12 13717530 rs74442473 2.53E-08 GRIN2B G G -1.02 0.360595 GRIN2B SNP-based Endophenotype 29274321 Caucasian ADNI 206 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr12 13763366 rs78210707 0.00000428 GRIN2B G G 0.38 0.38 GRIN2B SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD intron_variant chr12 13770394 rs11055612 0.00000281 GRIN2B T T -3371.6 0 GRIN2B SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr12 13770394 rs11055612 0.0000159 GRIN2B T T -3371.6 0 GRIN2B SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr12 13777923 rs10845840 0.000000126 GRIN2B T T -3802.2 0 GRIN2B SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr12 13777923 rs10845840 0.000000403 GRIN2B T T -3802.2 0 GRIN2B SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr12 21304500 rs11568563 0.00000007 SLCO1A2 NA NA 0.68 0.68 SLCO1A2 SNP-based Disease Risk 22685416 Caucasian "Cohorts from Europe, USA" 8851 All Progressive Supranuclear Palsy (PSP) ADRD missense_variant chr12 21304500 rs11568563 0.0000198 SLCO1A2 NR NR -0.44 0.644036 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 197 AD SLCO1A2 (ILMN_2381020) expression in Cerebellar Expression missense_variant chr12 21304500 rs11568563 0.0000389 SLCO1A2 NR NR -0.64 0.527292 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 107 PSP SLCO1A2 (ILMN_2381020) expression in Temporal cortex Expression missense_variant chr12 21304500 rs11568563 0.00362 SLCO1A2 NR NR -0.37 0.690734 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 98 PSP SLCO1A2 (ILMN_2381020) expression in Cerebellar Expression missense_variant chr12 21304500 rs11568563 0.0436 SLCO1A2 NR NR -0.12 0.88692 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 399 All SLCO1A2 (ILMN_1656097) expression in Temporal cortex Expression missense_variant chr12 21304500 rs11568563 0.212 SLCO1A2 NR NR -0.12 0.88692 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 197 AD SLCO1A2 (ILMN_1656097) expression in Cerebellar Expression missense_variant chr12 21304500 rs11568563 0.241 SLCO1A2 NR NR -0.08 0.923116 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 374 All SLCO1A2 (ILMN_1656097) expression in Cerebellar Expression missense_variant chr12 21304500 rs11568563 0.422 SLCO1A2 NR NR -0.06 0.941765 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 202 AD SLCO1A2 (ILMN_1656097) expression in Temporal cortex Expression missense_variant chr12 21304500 rs11568563 0.608 SLCO1A2 NR NR -0.06 0.941765 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 107 PSP SLCO1A2 (ILMN_1656097) expression in Temporal cortex Expression missense_variant chr12 21304500 rs11568563 0.814 SLCO1A2 NR NR -0.03 0.970446 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 98 PSP SLCO1A2 (ILMN_1656097) expression in Cerebellar Expression missense_variant chr12 21304500 rs11568563 1.23E-08 SLCO1A2 NR NR -0.72 0.486752 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 202 AD SLCO1A2 (ILMN_2381020) expression in Temporal cortex Expression missense_variant chr12 21304500 rs11568563 2.33E-08 SLCO1A2 NR NR -0.4 0.67032 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 374 All SLCO1A2 (ILMN_2381020) expression in Cerebellar Expression missense_variant chr12 21304500 rs11568563 9.14E-18 SLCO1A2 NR NR -0.73 0.481909 SLCO1A2 SNP-based eQTL 22685416 Caucasian MAYO 399 All SLCO1A2 (ILMN_2381020) expression in Temporal cortex Expression missense_variant chr12 21841177 rs704180 NR ABCC9 A A 1.13 1.13 ABCC9 SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr12 21841177 rs704180 NR ABCC9 A A 1.38 1.38 ABCC9 SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr12 21841177 rs704180 NR ABCC9 A A 1.46 1.46 ABCC9 SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr12 21841177 rs704180 NR ABCC9 A A 1.51 1.51 ABCC9 SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr12 21841177 rs704180 NR ABCC9 A A 1.9 1.9 ABCC9 SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr12 21841177 rs704180 NR ABCC9 A A 2 2 ABCC9 SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr12 21846929 rs829080 0.0057 ABCC9 C C 1.76 1.76 ABCC9 SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (DOM Model) Hippocampal sclerosis of aging ADRD intron_variant chr12 21851264 rs7966849 0.000000101 ABCC9 G G NR NA ABCC9 SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr12 21851264 rs7966849 0.0000071 ABCC9 A A 1.84 1.84 ABCC9 SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (REC Model) Hippocampal sclerosis of aging ADRD intron_variant chr12 21851264 rs7966849 0.000044 ABCC9 NR NR 1.46 1.46 ABCC9 SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (ADD Model) Hippocampal sclerosis of aging ADRD intron_variant chr12 29768734 rs302318 0.00000197 TMTC1 C C 0.59 0.59 TMTC1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr12 31088411 rs10843881 2.48E-52 DDX11 NR NR -1.06 0.346456 DDX11 SNP-based eQTL 22685416 Caucasian MAYO 197 AD DDX11 expression in Cerebellar Expression intron_variant chr12 31088411 rs10843881 3.49E-48 DDX11 NR NR -1.06 0.346456 DDX11 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD DDX11 expression in Cerebellar Expression intron_variant chr12 31088411 rs10843881 4.87E-110 DDX11 NR NR -1.16 0.313486 DDX11 SNP-based eQTL 22685416 Caucasian MAYO 399 All DDX11 expression in Temporal cortex Expression intron_variant chr12 31088411 rs10843881 6.57E-107 DDX11 NR NR -1.06 0.346456 DDX11 SNP-based eQTL 22685416 Caucasian MAYO 374 All DDX11 expression in Cerebellar Expression intron_variant chr12 38774384 rs10876062 0.0000387 CPNE8 NR NR 4.28 4.28 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38821850 rs12424244 0.0000411 CPNE8 NR NR 0.25 0.25 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38825216 rs17126713 0.0000399 CPNE8 NR NR 3.94 3.94 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38849391 rs9943730 0.000036 CPNE8 NR NR 0.25 0.25 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38856882 rs12425783 0.0000342 CPNE8 NR NR 4.04 4.04 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38863148 rs12422883 0.0000349 CPNE8 NR NR 4.03 4.03 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38864847 rs10876185 0.0000347 CPNE8 NR NR 0.25 0.25 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38891156 rs7308580 0.0000149 CPNE8 NR NR 0.18 0.18 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38891304 rs7307936 0.0000151 CPNE8 NR NR 5.6 5.6 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38903226 rs1516555 0.0000165 CPNE8 NR NR 5.55 5.55 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr12 38912965 rs12423647 0.0000301 NR NR NR 5.17 5.17 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD downstream_gene_variant chr12 38915912 rs1878224 0.000036 NR NR NR 5.08 5.08 CPNE8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD upstream_gene_variant chr12 39882501 rs75036080 0.00000307 SLC2A13 G G 0.49 0.49 C12orf40 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD intron_variant chr12 40051948 rs10784359 0.000158 SLC2A13 NR NR NR NA SLC2A13 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr12 43573874 rs7295246 0.00000027 ADAMTS20 G G 1.07 1.07 ADAMTS20 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD upstream_gene_variant chr12 43573874 rs7295246 0.00000039 ADAMTS20 G G 1.06 1.06 ADAMTS20 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD upstream_gene_variant chr12 43573874 rs7295246 0.325 ADAMST20 G G 1.044 1.044 ADAMTS20 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD upstream_gene_variant chr12 43573874 rs7295246 0.45 ADAMTS20 G G 1.02 1.02 ADAMTS20 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD upstream_gene_variant chr12 47245743 rs11610206 0.00000143 FAM113B NR NR NR NA PCED1B SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr12 49853685 rs7138803 0.277 NR A A 1.041 1.041 BCDIN3D SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr12 49853685 rs7138803 0.436 NR A A 0 1 BCDIN3D SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr12 49853685 rs7138803 0.549 NR A A 0.987 0.987 BCDIN3D SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr12 49853685 rs7138803 0.999 NR A A 1.094 1.094 BCDIN3D SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr12 53130475 rs77451327 0.000906 SOAT2 C C NR NA SOAT2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr12 53130475 rs77451327 0.00256 SOAT2 C C NR NA SOAT2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD upstream_gene_variant chr12 53130475 rs77451327 0.726 SOAT2 C C 1 1 SOAT2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD upstream_gene_variant chr12 53533770 rs784568 0.0073 ATF7 NR NR NR NA ATF7-NPFF SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr12 53664454 rs1971762 2.10E-103 ATP5G2 NR NR 1.15 3.15819 ATP5MC2 SNP-based eQTL 22685416 Caucasian MAYO 399 All ATP5G2 expression in Temporal cortex Expression intron_variant chr12 53664454 rs1971762 2.11E-53 ATP5G2 NR NR 1.04 2.82922 ATP5MC2 SNP-based eQTL 22685416 Caucasian MAYO 197 AD ATP5G2 expression in Cerebellar Expression intron_variant chr12 53664454 rs1971762 4.87E-99 ATP5G2 NR NR 1.01 2.7456 ATP5MC2 SNP-based eQTL 22685416 Caucasian MAYO 374 All ATP5G2 expression in Cerebellar Expression intron_variant chr12 53664454 rs1971762 6.73E-39 ATP5G2 NR NR 0.96 2.6117 ATP5MC2 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD ATP5G2 expression in Cerebellar Expression intron_variant chr12 53669709 rs1800634 0.0006 ATP5G2 NR NR NR NA ATP5MC2 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr12 56007301 rs10876864 8.07E-61 RPS26 NR NR 0.57 1.76827 IKZF4 SNP-based eQTL 22685416 Caucasian MAYO 399 All RPS26 expression in Temporal cortex Expression upstream_gene_variant chr12 56926927 rs840163 0.00000242 SDR9C7 G G 1.4 NA SDR9C7 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr12 57243810 rs3204635 0.00015 STAC3 NR NR NR NA STAC3 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD 3_prime_UTR_variant chr12 57243810 rs3204635 0.00086 STAC3 NR NR NR NA STAC3 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr12 57243810 rs3204635 0.0025 STAC3 NR NR NR NA STAC3 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD 3_prime_UTR_variant chr12 57243810 rs3204635 0.41 STAC3 NR NR NR NA STAC3 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD 3_prime_UTR_variant chr12 65271195 rs10878255 1.16E-59 LEMD3 NR NR -0.62 0.537944 MSRB3 SNP-based eQTL 22685416 Caucasian MAYO 374 All LEMD3 expression in Cerebellar Expression intergenic_region chr12 65271195 rs10878255 4.09E-30 LEMD3 NR NR -0.56 0.571209 MSRB3 SNP-based eQTL 22685416 Caucasian MAYO 197 AD LEMD3 expression in Cerebellar Expression intergenic_region chr12 65271195 rs10878255 4.65E-66 LEMD3 NR NR -0.78 0.458406 MSRB3 SNP-based eQTL 22685416 Caucasian MAYO 399 All LEMD3 expression in Temporal cortex Expression intergenic_region chr12 65271195 rs10878255 5.54E-24 LEMD3 NR NR -0.68 0.506617 MSRB3 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD LEMD3 expression in Cerebellar Expression intergenic_region chr12 65767191 rs10784496 0.000000309 NR G G NR NA HMGA2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr12 65818538 rs2261181 0.0000001 HMGA2 NR NR NR NA HMGA2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr12 66067239 rs35758766 0.00372 TMBIM4 A A NR NA LLPH SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD downstream_gene_variant chr12 66067239 rs35758766 2.16E-61 NR A A NR NA LLPH SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group TMBIM4 (ILMN_1664750) expression Expression downstream_gene_variant chr12 66181338 rs1436849 0.00125 IRAK3 T T NR NA IRAK3 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intergenic_region chr12 66181338 rs1436849 6.14E-35 NR T T NR NA IRAK3 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) IRAK3 (ILMN_1913678) expression in peripheral blood Expression intergenic_region chr12 71017781 rs7132840 0.000013 CHR12 NR NR NR NA PTPRR SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr12 84863448 rs3782369 0.049 SLC6A15 NR NR 12.25 12.25 SLC6A15 SNP-based Cross phenotype 30010129 Asian Cohort from Han Chinse 475 All AD AD missense_variant chr12 84870956 rs79265864 0.125 SLC6A15 NR NR NR NA SLC6A15 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr12 84870956 rs79265864 0.47453 NA NR NR NR NA SLC6A15 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr12 94930613 rs249153 0.000000438 NR C C 1.41 1.41 NDUFA12 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr12 94934697 rs249166 0.000000691 NR T T 1.4 1.4 NDUFA12 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr12 94936497 rs249167 0.000000691 NR A A 1.4 1.4 NDUFA12 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr12 101293265 rs2290720 0.00000284 UTP20 A A -148.1 4.79719e-65 UTP20 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intron_variant chr12 101293265 rs2290720 0.0000146 NR A A -148.1 4.79719e-65 UTP20 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intron_variant chr12 102529208 rs2195243 0.000000015 NR C C -0.06 0.941765 IGF1 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 26577 European Intracranial Volume Imaging intergenic_region chr12 102529208 rs2195243 0.101 NR C C -0.09 0.913931 IGF1 SNP-based Endophenotype 27694991 Hispanic "CHARGE, ENIGMA" 1605 Hispanic Intracranial Volume Imaging intergenic_region chr12 102529208 rs2195243 0.132 NR C C -0.04 0.960789 IGF1 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 2363 European Intracranial Volume Imaging intergenic_region chr12 102529208 rs2195243 0.585 NR C C 0.04 1.04081 IGF1 SNP-based Endophenotype 27694991 African American "CHARGE, ENIGMA" 938 African Intracranial Volume Imaging intergenic_region chr12 102529208 rs2195243 0.774 NR C C -0.02 0.980199 IGF1 SNP-based Endophenotype 27694991 Asian "CHARGE, ENIGMA" 955 Asian Intracranial Volume Imaging intergenic_region chr12 108342575 rs7304039 0.00000079 NR A A 0.41 1.50682 CMKLR1 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker upstream_gene_variant chr12 108342575 rs7304039 0.0069 NR A A 0.15 1.16183 CMKLR1 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker upstream_gene_variant chr12 108342575 rs7304039 0.34 NR A A -0.07 0.932394 CMKLR1 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker upstream_gene_variant chr12 108448599 rs66478310 0.00000486 LOC102723562 NR NR NR NA FICD SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intron_variant chr12 112403438 rs7972529 0.000352 RPL6 G G NR NA RPL6 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD downstream_gene_variant chr12 112403438 rs7972529 0.000449 RPL6 G G NR NA RPL6 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD downstream_gene_variant chr12 112996713 rs1635142 0.0000532 OAS2 A A NR NA OAS2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr12 112996713 rs1635142 0.00015 OAS2 A A 0.95 0.95 OAS2 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr12 112996713 rs1635142 0.000228 OAS2 A A NR NA OAS2 SNP-based Cross phenotype 30413934 Caucasian "GIANT, UKBB" 180423 All Waist-to-hip ratio (WHR) Non-ADRD intron_variant chr12 112996713 rs1635142 0.0005 OAS2 A A 0.95 0.95 OAS2 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr12 112996713 rs1635142 0.306 OAS2 A A 1 1 OAS2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr12 112996713 rs1635142 0.461 OAS2 A A 1.04 1.04 OAS2 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr12 114942588 rs10850408 0.000000925 NR T T 0.63 0.63 TBX3 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr12 115427498 rs10161338 0.0000352 Intergenic (as reported in paper) C C NR NA MED13L SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr12 115427498 rs10161338 0.0009 NR C C NR NA MED13L SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr12 115427498 rs10161338 0.00176 NR C C NR NA MED13L SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr12 116857528 rs17429217 0.00000257 "HRK, RNFT2" NR NR NR NA HRK SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other 3_prime_UTR_variant chr12 116857528 rs17429217 0.00000318 "HRK, RNFT2" NR NR NR NA HRK SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other 3_prime_UTR_variant chr12 116857528 rs17429217 0.000248 "HRK, RNFT2" NR NR 2.84 17.1158 HRK SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other 3_prime_UTR_variant chr12 116857528 rs17429217 0.004 "HRK, RNFT2" NR NR 2.44 11.473 HRK SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other 3_prime_UTR_variant chr12 116857528 rs17429217 0.503 "HRK, RNFT2" NR NR 4.76 116.746 HRK SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other 3_prime_UTR_variant chr12 117347106 rs2101238 0.00000956 NOS1 NR NR NR NA NOS1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr12 118455443 rs11613092 0.00000231 NR A A 0.41 0.41 SUDS3 SNP-based Disease risk 26049409 Asian Cohort from Japan 6944 e4 noncarrier LOAD AD intergenic_region chr12 118455443 rs11613092 0.00000685 NR A A 0.61 0.61 SUDS3 SNP-based Disease risk 26049409 Asian Cohort from Japan 13290 e4 noncarrier LOAD AD intergenic_region chr12 118455443 rs11613092 0.0356 NR A A 0.75 0.75 SUDS3 SNP-based Disease risk 26049409 Asian Cohort from Japan 6346 e4 noncarrier LOAD AD intergenic_region chr12 118930022 rs11069178 0.000000165 NR C C NR NA SRRM4 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr12 118950113 rs1997111 0.000000011 NR T T NR NA SRRM4 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr12 118950113 rs1997111 0.000000211 NR T T NR NA SRRM4 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr12 118952720 rs10775009 1.59E-09 SRRM4 T T 0.51 1.66529 SRRM4 SNP-based Endophenotype 29274321 Caucasian ADNI 203 Normal controls CSF T-tau Fluid biomarker intergenic_region chr12 123034319 rs641760 0.000275 ABCB9 T T NR NA PITPNM2 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intron_variant chr12 123034319 rs641760 9.79E-17 NR T T NR NA PITPNM2 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) ABCB9 (ILMN_2343047) expression Expression intron_variant chr12 130537465 rs1464108 0.00000819 RIMBP2 NR NR 1.28 1.28 RIMBP2 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intron_variant chr12 131542412 rs73156187 0.00000447 SFSWAP G G 0.7 0.7 SFSWAP SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intergenic_region chr12 131573284 rs7963314 0.00000272 SFSWAP G G 0.7 0.7 SFSWAP SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intergenic_region chr12 132630826 rs4883627 1.06E-15 POLE NR NR 0.22 1.24608 POLE SNP-based eQTL 22685416 Caucasian MAYO 399 All POLE expression in Temporal cortex Expression intron_variant chr13 21325916 rs12583648 0.000000233 "LINC00539, ZDHHC20" C C NR NA ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 20770 All Brain infarcts (BI) Imaging intron_variant chr13 21325916 rs12583648 0.0000295 "LINC00539, ZDHHC20" C C 1.2 1.2 ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 16690 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr13 21325916 rs12583648 0.0000408 "LINC00539, ZDHHC20" NR NR 1.11 1.11 ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 27632 All Brain infarcts (BI) Imaging intron_variant chr13 21325916 rs12583648 0.0000766 "LINC00539, ZDHHC20" C C NR NA ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 16690 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr13 21325916 rs12583648 0.00895 "LINC00539, ZDHHC20" NR NR 1.08 1.08 ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 23552 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr13 21325916 rs12583648 0.46 "LINC00539, ZDHHC20" NR NR 0.95 0.95 ZDHHC20 SNP-based Endophenotype 30651383 Caucasian ADGC 2940 All Pathologically defined infarcts Imaging intron_variant chr13 21325916 rs12583648 0.53 "LINC00539, ZDHHC20" NR NR 1.01 1.01 ZDHHC20 SNP-based Endophenotype 30651383 Caucasian "CHARGE, METASTROKE, SiGN" 137560 All Ischemic stroke (IS) Imaging intron_variant chr13 21325916 rs12583648 0.55 "LINC00539, ZDHHC20" NR NR 0.97 0.97 ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr13 21325916 rs12583648 0.63 "LINC00539, ZDHHC20" NR NR 0.98 0.98 ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Brain infarcts (BI) Imaging intron_variant chr13 21325916 rs12583648 0.86 "LINC00539, ZDHHC20" NR NR 1.01 1.01 ZDHHC20 SNP-based Endophenotype 30651383 Caucasian "METASTROKE, SiGN, YLSDR" 41039 All Ischemic stroke due to small vessel disease (IS-SVD) Imaging intron_variant chr13 21325916 rs12583648 5.82E-09 "LINC00539, ZDHHC20" C C 1.21 1.21 ZDHHC20 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 20770 All Brain infarcts (BI) Imaging intron_variant chr13 26150190 rs17511627 0.00000501 NR C C 1.75 1.75 RNF6 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr13 27446043 rs4771122 0.403 NR G G 0.961 0.961 MTIF3 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr13 27446043 rs4771122 0.672 NR G G 0.988 0.988 MTIF3 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr13 27852622 rs2387100 0.0000382 NR NR NR NR NA GSX1 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr13 32313252 rs4942417 0.0000021 NR C C 0.44 1.55271 ZAR1L SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker null chr13 32313252 rs4942417 0.0036 NR C C -0.19 0.826959 ZAR1L SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker null chr13 32313252 rs4942417 0.42 NR C C -0.08 0.923116 ZAR1L SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker null chr13 32572915 rs718444 0.00116 N4BP2L2 T T NR NA PDS5B SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intergenic_region chr13 32572915 rs718444 1.80E-53 NR T T NR NA PDS5B SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) N4BP2L2 (ILMN_1737561) expression in peripheral blood Expression intergenic_region chr13 34080781 rs690705 0.000000634 RFC3 NR NR NR NA RFC3 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD downstream_gene_variant chr13 34376390 rs17798800 0.00000684 NR A A 0.38 0.38 RFC3 SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 337 Probable AD "Responder (MMSE increased, remained stable, or the Delta MMSE fell by 1or less) vs Non-responder (worsening of >3 points in Delta MMSE)" Cognitive intron_variant chr13 34376390 rs17798800 0.0000823 NR A A -2.12 0.120032 RFC3 SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 337 Probable AD Delta MMSE (annualized difference between MMSE score at baseline and at follow-up) Cognitive intron_variant chr13 34376390 rs17798800 0.000124 NR A A 0.34 0.34 RFC3 SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 169 Probable AD "Responder (MMSE increased, remained stable, or the Delta MMSE fell by 1or less) vs Non-responder (worsening of >3 points in Delta MMSE)" Cognitive intron_variant chr13 34376390 rs17798800 0.00138 NR A A -2.38 0.0925506 RFC3 SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 169 Probable AD Delta MMSE (annualized difference between MMSE score at baseline and at follow-up) Cognitive intron_variant chr13 34376390 rs17798800 0.00878 NR A A 0.44 0.44 RFC3 SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 168 Probable AD "Responder (MMSE increased, remained stable, or the Delta MMSE fell by 1or less) vs Non-responder (worsening of >3 points in Delta MMSE)" Cognitive intron_variant chr13 34376390 rs17798800 0.0241 NR A A -1.82 0.162026 RFC3 SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 168 Probable AD Delta MMSE (annualized difference between MMSE score at baseline and at follow-up) Cognitive intron_variant chr13 43591883 rs17460623 0.00000937 ENOX1 C C 0.49 0.49 ENOX1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr13 45942333 rs741668 0.00000464 ZC3H13 NR NR 0.27 1.30996 ZC3H13 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intergenic_region chr13 45942333 rs741668 0.0002 ZC3H13 NR NR 0.3 1.34986 ZC3H13 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intergenic_region chr13 45942333 rs741668 0.00749 ZC3H13 NR NR 0.23 1.2586 ZC3H13 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intergenic_region chr13 49533153 rs1046028 1.44E-79 PHF11 NR NR 0.38 1.46228 RCBTB1 SNP-based eQTL 22685416 Caucasian MAYO 399 All PHF11 expression in Temporal cortex Expression 3_prime_UTR_variant chr13 49533153 rs1046028 4.73E-70 PHF11 NR NR 0.35 1.41907 RCBTB1 SNP-based eQTL 22685416 Caucasian MAYO 374 All PHF11 expression in Cerebellar Expression 3_prime_UTR_variant chr13 49533153 rs1046028 4.79E-29 PHF11 NR NR 0.37 1.44773 RCBTB1 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD PHF11 expression in Cerebellar Expression 3_prime_UTR_variant chr13 49533153 rs1046028 5.61E-35 PHF11 NR NR 0.33 1.39097 RCBTB1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD PHF11 expression in Cerebellar Expression 3_prime_UTR_variant chr13 51272469 rs1006064 0.00000502 FAM124A NR NR 0.252 1.2866 FAM124A SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr13 51272469 rs1006064 0.000143 FAM124A NR NR 0.283 1.32711 FAM124A SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr13 51272469 rs1006064 0.00799 FAM124A NR NR 0.216 1.2411 FAM124A SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr13 52656848 rs4885767 0.00079 SUGT1 NR NR NR NA SUGT1 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr13 52656848 rs4885767 0.00197 NA NR NR NR NA SUGT1 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr13 52930540 rs9527039 0.000000564 GLIS1 NR NR 0.08 1.08329 PCDH8 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF P-tau181p Fluid biomarker intergenic_region chr13 52930540 rs9527039 0.000011 GLIS1 C C 0.05 1.05127 PCDH8 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF T-tau Fluid biomarker intergenic_region chr13 52930540 rs9527039 0.002 GLIS1 NR NR 0.05 1.05127 PCDH8 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF P-tau181p Fluid biomarker intergenic_region chr13 52930540 rs9527039 0.0424 GLIS1 C C 0.02 1.0202 PCDH8 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF Ab1-42 Fluid biomarker intergenic_region chr13 52930540 rs9527039 0.403 GLIS1 C C 0.02 1.0202 PCDH8 SNP-based Age at onset (AAO) / Survival 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 39855 AD subjects Age at onset Other intergenic_region chr13 52930540 rs9527039 0.425 GLIS1 C C 0.069 1.07144 PCDH8 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1530 All AD Progression (based on CDR Score) Cognitive intergenic_region chr13 52930540 rs9527039 0.822 GLIS1 C C 0.99 2.69123 PCDH8 SNP-based Disease risk 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 74046 All AD risk AD intergenic_region chr13 52930540 rs9527039 5.95E-09 GLIS1 C C 0.061 1.0629 PCDH8 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF P-tau181p Fluid biomarker intergenic_region chr13 52930540 rs9527039 5.95E-09 GLIS1 NR NR 0.06 1.06184 PCDH8 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF P-tau181p Fluid biomarker intergenic_region chr13 53039196 rs3803259 0.0326 OLFM4 NR NR NR NA OLFM4 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr13 53039196 rs3803259 0.3996 NA NR NR NR NA OLFM4 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr13 59271334 rs80155385 0.00000495 NR C C NR NA DIAPH3 SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intergenic_region chr13 70846292 rs1328032 0.000000193 DACH1 A A 0.67 0.67 DACH1 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intergenic_region chr13 70846292 rs1328032 0.0000739 DACH1 A A 0.8 0.8 DACH1 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intergenic_region chr13 70846292 rs1328032 0.34 DACH1 A A 0.94 0.94 DACH1 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intergenic_region chr13 75984017 rs9544105 0.00000541 NR NR NR NR NA LMO7 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intergenic_region chr13 76651467 rs9530579 0.985 NR NR NR NR NA KCTD12 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intergenic_region chr13 76736658 rs9600764 0.0000998 Intergenic (as reported in paper) G G NR NA KCTD12 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr13 76736658 rs9600764 0.00019 NR G G NR NA KCTD12 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr13 76736658 rs9600764 0.0027 NR G G NR NA KCTD12 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr13 76889101 rs659628 0.0000446 KCTD12 NR NR NR NA KCTD12 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD upstream_gene_variant chr13 89362235 rs7995618 0.0000041 LOC160824 NR NR NR NA SLITRK5 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker non_coding_transcript_exon_variant chr13 89869274 rs7331792 0.000469 BC038529 A A NR NA GPC5 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intergenic_region chr13 89869274 rs7331792 0.00125 BC038529 A A NR NA GPC5 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr13 91176054 rs61023801 0.00000047 NR G G 0.52 1.68203 GPC5 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF Ab1-42 Fluid biomarker intergenic_region chr13 91176054 rs61023801 0.0003 NR G G 0.52 1.68203 GPC5 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker intergenic_region chr13 91177310 rs74922937 0.92 NR A A 0.02 1.0202 GPC5 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intergenic_region chr13 98479040 rs912330 0.00000379 STK24 T T 0.54 0.54 STK24 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr13 101393128 rs11617026 0.0000017 NR NR NR NR NA NALCN SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr13 101393128 rs11617026 0.000055 NR NR NR 0.21 0.21 NALCN SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr13 101393128 rs11617026 0.000912 NR NR NR NR NA NALCN SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr13 101393128 rs11617026 0.0199 NR NR NR 0.54 0.54 NALCN SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr13 101393128 rs11617026 0.29264 NR NR NR NR NA NALCN SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr13 101393128 rs11617026 0.381 NR NR NR NR NA NALCN SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr13 101393128 rs11617026 0.445 NR NR NR NR NA NALCN SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr13 101393128 rs11617026 0.81524 NR NR NR NR NA NALCN SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr13 101393128 rs11617026 1 NR NR NR 0.82 0.82 NALCN SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr13 103011595 rs16961023 0.000000103 SLC10A2 G G 0.41 1.50682 SLC10A2 SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD liability score AD intergenic_region chr13 103011595 rs16961023 0.000000801 SLC10A2 G G 2.77 2.77 SLC10A2 SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD AD intergenic_region chr13 103011595 rs16961023 0.00000792 SLC10A2 G G 2.68 2.68 SLC10A2 SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD AD intergenic_region chr13 103011595 rs16961023 4.59E-08 SLC10A2 G G 0.41 1.50682 SLC10A2 SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD liability score AD intergenic_region chr13 106414855 rs2893253 0.000202 EFNB2 NR NR NR NA EFNB2 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intergenic_region chr13 109152426 rs9555561 0.00000253 MYO16 C C 1.25 1.25 MYO16 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intron_variant chr13 109155938 rs912322 0.00000129 MYO16 A A 1.26 1.26 MYO16 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intron_variant chr13 112951220 rs61963560 0.000592 BC035340 A A NR NA MCF2L SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr13 112951220 rs61963560 0.000758 BC035340 A A 0.94 0.94 MCF2L SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr13 112951220 rs61963560 0.00194 BC035340 A A NR NA MCF2L SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr13 112951220 rs61963560 0.00579 BC035340 A A 0.95 0.95 MCF2L SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr13 112951220 rs61963560 0.0743 BC035340 A A 1.13 1.13 MCF2L SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr13 112951220 rs61963560 0.867 BC035340 A A 1 1 MCF2L SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr13 113116562 rs488703 0.00000002 F7 NR NR -0.1 0.904837 F7 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma FactorVII Fluid biomarker intron_variant chr13 113116562 rs488703 0.042 F7 NR NR -118.18 4.73236e-52 F7 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma FactorVII Fluid biomarker intron_variant chr13 114070327 rs7981577 0.000137 RASA3 C C NR NA RASA3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr13 114070327 rs7981577 0.00228 RASA3 C C NR NA RASA3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr13 114070327 rs7981577 0.0956 RASA3 C C 0.98 0.98 RASA3 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr13 114070327 rs7981577 0.0976 RASA3 C C 0.98 0.98 RASA3 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr13 114070327 rs7981577 0.344 RASA3 C C 1 1 RASA3 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr13 114070327 rs7981577 0.834 RASA3 C C 0.99 0.99 RASA3 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr14 23932540 rs10483284 0.00701 DHRS4L2 T T NR NA DHRS4 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr14 23932540 rs10483284 5.36E-38 NR T T NR NA DHRS4 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group DHRS4L2 (ILMN_1761450) expression Expression intron_variant chr14 30045906 rs11847697 0.112 NR T T 0.835 0.835 PRKD1 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr14 30045906 rs11847697 0.671 NR T T 1.03 1.03 PRKD1 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr14 32483161 rs4296166 0.00000408 AKAP6 A A 1.12 1.12 AKAP6 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intron_variant chr14 32483161 rs4296166 0.0000836 AKAP6 A A 1.14 1.14 AKAP6 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intron_variant chr14 32483161 rs4296166 NR AKAP6 A A 0.98 0.98 AKAP6 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intron_variant chr14 32911892 rs12146962 0.00000725 NR NR NR NR NA NPAS3 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intergenic_region chr14 33841207 rs10149826 0.00000915 NPAS3 T T 0.22 1.24608 NPAS3 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intergenic_region chr14 39349412 rs8018486 0.00000115 "CTAGE5, FBXO33" G G NR NA MIA2 SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr14 52773317 rs73298734 0.00000169 GNPNAT1 NR NR 1.23 1.23 STYX SNP-based Disease risk 30979435 Caucasian ADGC 14297 Age 60-79 y AD AD 3_prime_UTR_variant chr14 52773317 rs73298734 0.455 GNPNAT1 NR NR 0.95 0.95 STYX SNP-based Disease risk 30979435 Caucasian ADGC 6311 Age >=80 y AD AD 3_prime_UTR_variant chr14 52886736 rs6572869 0.01 FERMT2 NR NR -0.11 NA FERMT2 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr14 52890300 rs62003531 0.0006 FERMT2 NR NR 0.02745 1.02783 FERMT2 SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr14 52899098 rs11157934 0.348 FERMT2 A A 1.06 NA FERMT2 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr14 52924962 rs17125924 0.00000066 FERMT2 G G 1.13 1.13 FERMT2 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr14 52924962 rs17125924 0.0000148 FERMT2 G G NR NA FERMT2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr14 52924962 rs17125924 0.0005 FERMT2 G G 1.15 1.15 FERMT2 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr14 52924962 rs17125924 0.00117 FERMT2 G G NR NA FERMT2 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr14 52924962 rs17125924 0.00147 FERMT2 G G 1.01 1.01 FERMT2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr14 52924962 rs17125924 0.769 FERMT2 G G 1.03 1.03 FERMT2 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr14 52924962 rs17125924 1.40E-09 FERMT2 G G 1.14 1.14 FERMT2 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr14 52924962 rs17125924 1.55E-08 FERMT2 G G 1.13 1.13 FERMT2 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr14 52924962 rs17125924 2.62E-08 FERMT2 G G 1.13 1.13 FERMT2 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr14 52933911 rs17125944 0.00001 FERMT2 C C 1.13 1.13 FERMT2 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr14 52933911 rs17125944 0.00016 FERMT2 C C 1.17 1.17 FERMT2 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr14 52933911 rs17125944 0.0185 FERMT2 C C 1.238 1.238 FERMT2 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr14 52933911 rs17125944 0.029 FERMT2 C C 1.22 1.22 FERMT2 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr14 52933911 rs17125944 0.036 FERMT2 C C 1.22 1.22 FERMT2 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr14 52933911 rs17125944 0.069 FERMT2 C C 1.27 1.27 FERMT2 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr14 52933911 rs17125944 0.085 FERMT2 C C 1.2 1.2 FERMT2 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr14 52933911 rs17125944 0.73 FERMT2 NR NR 0.94 0.94 FERMT2 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr14 52933911 rs17125944 7.90E-09 FERMT2 C C 1.14 1.14 FERMT2 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr14 52933911 rs17125944 NR FERMT2 C C 1.69 1.69 FERMT2 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr14 52933911 rs17125944 NR ZCWPW1 C C 1.41 1.41 FERMT2 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr14 52933911 rs17125944 NR ZCWPW1 C C 3.05 3.05 FERMT2 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr14 57548363 rs187911 0.00000623 SLC35F4 G G -0.14 0.869358 SLC35F4 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intergenic_region chr14 73198145 rs165932 0.121 PSEN1 G G 0.89 0.89 PSEN1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr14 73213398 rs3025787 0.003 PSEN1 G G 0.71 0.71 PSEN1 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1335 All Age of AD onset Other intron_variant chr14 73213398 rs3025787 0.04 PSEN1 G G 0.69 0.69 PSEN1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1335 All AD AD intron_variant chr14 73809286 rs17182607 0 NR A A NR NA MIDEAS SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group LOC100506476 (ENSG00000259065) expression Expression intergenic_region chr14 73809286 rs17182607 0.00478 LOC100506476 A A NR NA MIDEAS SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr14 74606345 rs2043948 0.000000444 LTBP2 T T 1.27 1.27 LTBP2 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intron_variant chr14 74606345 rs2043948 0.000446 LTBP2 T T 1.13 1.13 LTBP2 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intron_variant chr14 74606345 rs2043948 0.000696 LTBP2 T T 1.25 1.25 LTBP2 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intron_variant chr14 74643734 rs888417 0.00000409 LTBP2 NR NR NR NA AREL1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr14 74812336 rs10483861 0.0054 YLPM1 NR NR NR NA YLPM1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr14 78308963 rs7155434 0.00000782 KIAA0743 C C 3643 inf NRXN3 SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr14 78308963 rs7155434 0.00000795 KIAA0743 C C 3643 inf NRXN3 SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr14 79470621 rs10150332 0.379 NR C C 0.963 0.963 NRXN3 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr14 79470621 rs10150332 0.476 NR C C 1.02 1.02 NRXN3 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr14 79470621 rs10150332 0.55 NR C C 0.97 0.97 NRXN3 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr14 79470621 rs10150332 0.848 NR C C 0 1 NRXN3 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr14 79775873 rs17764668 0.00000984 NRXN3 NR NR NR NA NRXN3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr14 79775873 rs17764668 0.0000208 NRXN3 NR NR NR NA NRXN3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr14 79775873 rs17764668 0.00114 NRXN3 NR NR 1.15 3.15819 NRXN3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intron_variant chr14 79775873 rs17764668 0.00365 NRXN3 NR NR 1.14 3.12677 NRXN3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intron_variant chr14 79775873 rs17764668 0.437 NRXN3 NR NR 2.72 15.1803 NRXN3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intron_variant chr14 89310401 rs3783863 0.00000453 FOXN3 NR NR 0.575 1.77713 FOXN3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr14 89310401 rs3783863 0.0000814 FOXN3 NR NR 0.608 1.83675 FOXN3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr14 89310401 rs3783863 0.0241 FOXN3 NR NR 0.496 1.64214 FOXN3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr14 91419362 rs1285850 0.000031 "CCDC88C, SMEK1" NR NR NR NA CCDC88C SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr14 91725006 rs3814837 0.00000326 CATSPERB C C 0.64 0.64 CATSPERB SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr14 92460608 rs10498633 0.000000147 SLC24A4 NR NR NR NA SLC24A4 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr14 92460608 rs10498633 0.00000015 "RIN3, SLC24A4" T T 0.9 0.9 SLC24A4 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr14 92460608 rs10498633 0.0078 "RIN3, SLC24A4" T T 0.93 0.93 SLC24A4 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr14 92460608 rs10498633 0.043 "RIN3, SLC24A4" T T 0.88 0.88 SLC24A4 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr14 92460608 rs10498633 0.045 "RIN3, SLC24A4" T T 0.88 0.88 SLC24A4 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr14 92460608 rs10498633 0.14 "RIN3, SLC24A4" NR NR 0.86 0.86 SLC24A4 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr14 92460608 rs10498633 0.142 SLC24A4 T T 0.922 0.922 SLC24A4 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr14 92460608 rs10498633 0.31 "RIN3, SLC24A4" T T 0.93 0.93 SLC24A4 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr14 92460608 rs10498633 0.72 "RIN3, SLC24A4" T T 1.03 1.03 SLC24A4 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr14 92460608 rs10498633 5.50E-09 "RIN3, SLC24A4" T T 0.91 0.91 SLC24A4 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr14 92460608 rs10498633 NR "RIN3, SLC24A4" G G 1.24 1.24 SLC24A4 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr14 92460608 rs10498633 NR ZCWPW1 G G 1.15 1.15 SLC24A4 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr14 92460608 rs10498633 NR ZCWPW1 G G 1.5 1.5 SLC24A4 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr14 92466484 rs12881735 0.00000049 SLC24A4 C C 0.92 0.92 SLC24A4 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr14 92466484 rs12881735 0.0043 SLC24A4 C C 0.92 0.92 SLC24A4 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr14 92466484 rs12881735 7.40E-09 SLC24A4 C C 0.92 0.92 SLC24A4 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr14 92467776 rs12590273 0.000316 SLC24A4 NR NR 0.1 NA SLC24A4 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr14 92472511 rs12590654 0.0000037 SLC24A4 A A NR NA SLC24A4 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr14 92472511 rs12590654 1.65E-10 SLC24A4 A A -6.39 NA SLC24A4 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr14 92472511 rs12590654 1.98E-08 SLC24A4 A A NR NA SLC24A4 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr14 92526992 rs7160605 0.00405 RIN3 C C 1.35 NA RIN3 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr14 92649779 rs11621843 0.00000519 RIN3 G G 1.47 1.47 RIN3 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr14 92649779 rs11621843 0.00081 RIN3 G G 1.21 1.21 RIN3 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intron_variant chr14 92649779 rs11621843 0.72 RIN3 G G 1.03 1.03 RIN3 SNP-based Disease risk 23565137 Asian Cohort from Japan 1870 All LOAD AD intron_variant chr14 94397299 rs7151526 0.000000744 SERPINA1 NR NR -0.06 0.941765 SERPINA1 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma AAT Fluid biomarker intergenic_region chr14 94689439 rs11622883 0.000094 NR NR NR 1.19 1.19 AL049839.2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD intergenic_region chr14 94689439 rs11622883 0.01 NR NR NR NR NA AL049839.2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD intergenic_region chr14 94689439 rs11622883 0.033 NR NR NR NR NA AL049839.2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD intergenic_region chr14 94689439 rs11622883 0.091 NR NR NR NR NA AL049839.2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD intergenic_region chr14 94689439 rs11622883 0.144 NR NR NR NR NA AL049839.2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD intergenic_region chr14 94689439 rs11622883 0.339 GWA_14q32.13 A A 1.07 1.07 AL049839.2 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intergenic_region chr14 94689439 rs11622883 0.979 NR NR NR NR NA AL049839.2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD intergenic_region chr14 94895934 rs10484049 0.0000302 GSC NR NR NR NA GSC SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intergenic_region chr14 99570681 rs2400749 0.00000225 CCDC85C G G 0.72 NA CCDC85C SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr14 104919015 rs2819438 6.94E-09 "C14orf79,PLD4" A A -0.8 0.449329 PLD4 SNP-based Endophenotype 29274321 Caucasian ADNI 203 Normal controls CSF T-tau Fluid biomarker intergenic_region chr14 106514189 rs9324088 0.0002 NR G G NR NA TMEM121 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr14 106514189 rs9324088 0.0003 Intergenic (as reported in paper) G G NR NA TMEM121 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr14 106514189 rs9324088 0.013 NR G G NR NA TMEM121 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr14 106704673 rs7145100 0.1 abParts NR NR 0.08 NA TMEM121 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other upstream_gene_variant chr14 106825769 rs7140253 0.0000318 Intergenic (as reported in paper) G G NR NA TMEM121 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD upstream_gene_variant chr14 106825769 rs7140253 0.00024 NR G G NR NA TMEM121 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD upstream_gene_variant chr14 106825769 rs7140253 0.0007 NR G G NR NA TMEM121 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD upstream_gene_variant chr15 36901080 rs4924109 0.00348 MEIS2 NR NR NR NA MEIS2 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr15 36901080 rs4924109 0.0503 NA NR NR NR NA MEIS2 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr15 37949388 rs112187315 0.179 TMCO5A NR NR NR NA TMCO5A SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr15 37949388 rs112187315 0.69431 NA NR NR NR NA TMCO5A Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr15 41993297 rs12232304 0.0000075 PLA2G4E NR NR NR NA PLA2G4E SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr15 50140297 rs10519262 0.00000448 NR A A 1.89 1.89 ATP8B4 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1321 AD subjects Age of AD onset Other intron_variant chr15 50140297 rs10519262 0.0332 NR A A 1.45 1.45 ATP8B4 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian MRC 554 AD subjects Age of AD onset Other intron_variant chr15 50438957 rs3131575 0.0000374 USP8 G G 0.93 0.93 USP8 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr15 50438957 rs3131575 0.000213 USP8 G G 0.94 0.94 USP8 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr15 50438957 rs3131575 0.000434 USP8 G G NR NA USP8 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr15 50438957 rs3131575 0.000459 USP8 G G NR NA USP8 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr15 50438957 rs3131575 0.0379 USP8 G G 1 1 USP8 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr15 50438957 rs3131575 0.352 USP8 G G 1.06 1.06 USP8 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr15 50510070 rs3131609 0.00000039 USP50 C C 0.93 0.93 USP8 SNP-based Disease risk 25862742 Caucasian IGAP 74046 All AD AD intron_variant chr15 50510070 rs3131609 0.000000721 USP50 C C 0.93 0.93 USP8 SNP-based Disease risk 25862742 Caucasian "deCODE, DemGene, IGAP" 143878 All AD AD intron_variant chr15 50510070 rs3131609 0.94 USP50 C C 1 1 USP8 SNP-based Disease risk 25862742 Caucasian deCODE 67817 All AD AD intron_variant chr15 50510070 rs3131609 0.95 USP50 C C 0.99 0.99 USP8 SNP-based Disease risk 25862742 Caucasian DemGene 2015 All AD AD intron_variant chr15 50716490 rs10467994 0.00000039 SPPL2A C C 0.94 0.94 SPPL2A SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr15 50716490 rs10467994 0.00000043 SPPL2A C C 0.94 0.94 SPPL2A SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD intron_variant chr15 50716490 rs10467994 0.62 SPPL2A C C 0.97 0.97 SPPL2A SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD intron_variant chr15 50748601 rs8035452 0.031 SPPL2A C C 1.102 1.102 SPPL2A SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr15 51223858 rs2899472 0.000000054 CYP19A1 A A 0.18 1.19722 CYP19A1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr15 51223858 rs2899472 0.000000111 CYP19A1 A A -0.14 0.869358 CYP19A1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr15 51223858 rs2899472 1.86E-09 CYP19A1 A A NR NA CYP19A1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr15 51223858 rs2899472 1.90E-12 CYP19A1 A A NR NA CYP19A1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr15 51223858 rs2899472 3.85E-10 CYP19A1 A A -0.14 0.869358 CYP19A1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr15 51223858 rs2899472 4.15E-09 CYP19A1 A A 0.16 1.17351 CYP19A1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr15 51387586 rs2446406 0.000000718 GLDN A A 0.81 0.81 GLDN SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intron_variant chr15 51387586 rs2446406 0.0000224 GLDN A A 0.87 0.87 GLDN SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr15 51387586 rs2446406 0.4 GLDN A A 0.96 0.96 GLDN SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intron_variant chr15 58730416 rs442495 0.000000265 ADAM10 C C NR NA ADAM10 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr15 58730416 rs442495 0.000309 ADAM10 C C NR NA ADAM10 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr15 58730416 rs442495 1.31E-09 ADAM10 C C -6.07 NA ADAM10 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr15 58753575 rs593742 0.00000013 ADAM10 G G 0.93 0.93 ADAM10 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD upstream_gene_variant chr15 58753575 rs593742 0.015 ADAM10 G G 0.91 0.91 ADAM10 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD upstream_gene_variant chr15 58753575 rs593742 6.20E-11 NR A A 1.06 1.06 ADAM10 SNP-based Disease risk 29777097 Caucasian UKBB 623001 All AD AD upstream_gene_variant chr15 58753575 rs593742 6.80E-09 ADAM10 G G 0.93 0.93 ADAM10 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD upstream_gene_variant chr15 58768943 rs650366 0.000000448 FAM63B G G 0.99 0.99 MINDY2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr15 58768943 rs650366 0.000654 FAM63B G G NR NA MINDY2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr15 58768943 rs650366 0.000686 FAM63B G G NR NA MINDY2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr15 61879280 rs1981916 0.0016 VPS13C NR NR NR NA VPS13C SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr15 62395140 rs2456930 0.00000015 NR A A 3843.9 inf TLN2 SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr15 62395140 rs2456930 0.000000314 NR A A 3843.9 inf TLN2 SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intron_variant chr15 63277703 rs117618017 0.000000264 APH1B T T NR NA APH1B SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD missense_variant chr15 63277703 rs117618017 0.022 APH1B T T NR NA APH1B SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD missense_variant chr15 63277703 rs117618017 3.35E-08 APH1B T T 5.52 NA APH1B SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD missense_variant chr15 64383114 rs11635527 0.00661 TRIP4 G G 1.46 NA PCLAF SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr15 64433291 rs74615166 0.000794 TRIP4 NR NR -0.23 NA TRIP4 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr15 64433291 rs74615166 0.00327 TRIP4 C C 1.519 1.519 TRIP4 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr15 67794500 rs2241423 0.043 NR G G 0.01 1.01005 MAP2K5 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr15 67794500 rs2241423 0.295 NR G G 0.951 0.951 MAP2K5 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr15 67794500 rs2241423 0.367 NR G G 0.964 0.964 MAP2K5 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr15 67794500 rs2241423 0.855 NR G G 0.995 0.995 MAP2K5 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr15 78540007 rs56117933 0.00083 PSMA4 NR NR NR NA PSMA4 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr15 78540007 rs56117933 0.56 PSMA4 NR NR NR NA PSMA4 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD upstream_gene_variant chr15 78540007 rs56117933 4.10E-20 PSMA4 NR NR NR NA PSMA4 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD upstream_gene_variant chr15 78540007 rs56117933 <2.2E-16 PSMA4 NR NR NR NA PSMA4 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD upstream_gene_variant chr15 80347061 rs3843702 0.00013 LINC00927 NR NR NR NA ARNT2 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intron_variant chr15 80347061 rs3843702 0.00087 LINC00927 NR NR NR NA ARNT2 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intron_variant chr15 80347061 rs3843702 0.0025 LINC00927 NR NR NR NA ARNT2 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intron_variant chr15 80347061 rs3843702 0.44 LINC00927 NR NR NR NA ARNT2 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intron_variant chr15 81299298 rs4778636 0.00383 IL16 NR NR -74.1 6.58838e-33 IL16 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma IL-16 Fluid biomarker splice_region_variant&intron_variant chr15 81299298 rs4778636 5.08E-19 IL16 NR NR -0.16 0.852144 IL16 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma IL-16 Fluid biomarker splice_region_variant&intron_variant chr15 81948683 rs11630802 0.00000488 NR NR NR NR NA MEX3B SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD downstream_gene_variant chr15 81948683 rs11630802 0.000127 NR NR NR 0.66 0.66 MEX3B SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD downstream_gene_variant chr15 81948683 rs11630802 0.000706 NR NR NR NR NA MEX3B SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD downstream_gene_variant chr15 81948683 rs11630802 0.00185 NR NR NR NR NA MEX3B SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD downstream_gene_variant chr15 81948683 rs11630802 0.0156 NR NR NR 0.58 0.58 MEX3B SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD downstream_gene_variant chr15 81948683 rs11630802 0.0383 NR NR NR 0.71 0.71 MEX3B SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD downstream_gene_variant chr15 81948683 rs11630802 NA NR NR NR NR NA MEX3B SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD downstream_gene_variant chr15 81948683 rs11630802 NA NR NR NR NR NA MEX3B SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD downstream_gene_variant chr15 84887738 rs3743162 0.00000868 "ALPK3, SLC28A1, ZNF592" NR NR NR NA SLC28A1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other splice_region_variant&intron_variant chr15 84887738 rs3743162 0.0000999 "ALPK3, SLC28A1, ZNF592" NR NR NR NA SLC28A1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other splice_region_variant&intron_variant chr15 84887738 rs3743162 0.000602 "ALPK3, SLC28A1, ZNF592" NR NR -1.03 0.357007 SLC28A1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other splice_region_variant&intron_variant chr15 84887738 rs3743162 0.0057 "ALPK3, SLC28A1, ZNF592" NR NR -0.88 0.414783 SLC28A1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other splice_region_variant&intron_variant chr15 84887738 rs3743162 0.496 "ALPK3, SLC28A1, ZNF592" NR NR -1.84 0.158817 SLC28A1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other splice_region_variant&intron_variant chr15 88857108 rs2882676 0.001 AGC1 NR NR 1.07 1.07 ACAN SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD missense_variant chr15 88857108 rs2882676 0.033 AGC1 NR NR NR NA ACAN SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD missense_variant chr15 88857108 rs2882676 0.05 AGC1 NR NR NR NA ACAN SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD missense_variant chr15 88857108 rs2882676 0.076 AGC1 NR NR NR NA ACAN SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD missense_variant chr15 88857108 rs2882676 0.358 AGC1 NR NR NR NA ACAN SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD missense_variant chr15 88857108 rs2882676 0.375 AGC1 NR NR NR NA ACAN SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD missense_variant chr15 90087660 rs9972327 0.00000562 IDH2 NR NR 0.4 1.49182 IDH2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr15 90087660 rs9972327 0.0000174 IDH2 NR NR 0.531 1.70063 IDH2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr15 90087660 rs9972327 0.0147 IDH2 NR NR 0.299 1.34851 IDH2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr15 91221762 rs74587705 0.000000336 SV2B T T 1.85 1.85 SV2B SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 8363 All Brain infarcts (BI) Imaging intron_variant chr15 91221762 rs74587705 0.00000569 SV2B T T NR NA SV2B SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 8363 All Brain infarcts (BI) Imaging intron_variant chr15 91221762 rs74587705 0.000582 SV2B NR NR 1.25 1.25 SV2B SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 15225 All Brain infarcts (BI) Imaging intron_variant chr15 91221762 rs74587705 0.39 SV2B NR NR 1.19 1.19 SV2B SNP-based Endophenotype 30651383 Caucasian ADGC 2940 All Pathologically defined infarcts Imaging intron_variant chr15 91221762 rs74587705 0.41 SV2B NR NR 1.07 1.07 SV2B SNP-based Endophenotype 30651383 Caucasian "METASTROKE, SiGN, YLSDR" 41039 All Ischemic stroke due to small vessel disease (IS-SVD) Imaging intron_variant chr15 91221762 rs74587705 0.41 SV2B NR NR 1.07 1.07 SV2B SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Brain infarcts (BI) Imaging intron_variant chr15 91221762 rs74587705 0.9 SV2B NR NR 1.01 1.01 SV2B SNP-based Endophenotype 30651383 Caucasian "CHARGE, METASTROKE, SiGN" 137560 All Ischemic stroke (IS) Imaging intron_variant chr15 91221762 rs74587705 0.92 SV2B NR NR 1.01 1.01 SV2B SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr15 97396008 rs4555132 0.0000308 NR NR NR NR NA ARRDC4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr15 98172432 rs1480090 0.0000352 NR NR NR NR NA ARRDC4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr15 98174448 rs1383139 0.0000348 NR NR NR NR NA ARRDC4 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr15 101646763 rs139709573 0.000000059 TM2D3 NR NR 8.62 8.62 TM2D3 SNP-based Disease risk 27764101 Caucasian AGES 2517 All LOAD AD missense_variant chr15 101646763 rs139709573 0.000000068 TM2D3 NR NR NR NA TM2D3 SNP-based Disease risk 27764101 Caucasian AGES 4336 All LOAD AD missense_variant chr15 101646763 rs139709573 0.000000084 TM2D3 NR NR NR NA TM2D3 SNP-based Disease risk 27764101 Caucasian AGES 2517 All LOAD AD missense_variant chr15 101646763 rs139709573 0.003 TM2D3 NR NR 5.42 5.42 TM2D3 SNP-based Disease risk 27764101 Caucasian AGES 1819 All LOAD AD missense_variant chr15 101646763 rs139709573 0.011 TM2D3 NR NR NR NA TM2D3 SNP-based Disease risk 27764101 Caucasian AGES 1819 All LOAD AD missense_variant chr15 101646763 rs139709573 6.60E-09 TM2D3 NR NR 7.45 7.45 TM2D3 SNP-based Disease risk 27764101 Caucasian AGES 4336 All LOAD AD missense_variant chr16 3687374 rs79848897 0.011 CREBBP C C 0.08 1.08329 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3687374 rs79848897 0.103 CREBBP C C -0.08 0.923116 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3687374 rs79848897 0.151 CREBBP C C 0.04 1.04081 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3687374 rs79848897 0.966 CREBBP C C 0 1 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3688077 rs2108430 0.028 CREBBP T T -0.1 0.904837 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3688077 rs2108430 0.063 CREBBP T T 0.06 1.06184 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3688077 rs2108430 0.595 CREBBP T T 0.01 1.01005 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3688077 rs2108430 0.751 CREBBP T T 0.02 1.0202 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3688285 rs72778151 0.019 CREBBP T T 0.08 1.08329 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3688285 rs72778151 0.114 CREBBP T T -0.1 0.904837 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3688285 rs72778151 0.157 CREBBP T T 0.04 1.04081 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3688285 rs72778151 0.506 CREBBP T T 0.02 1.0202 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3692347 rs36099109 0.006 CREBBP T T 0.09 1.09417 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3692347 rs36099109 0.043 CREBBP T T -0.12 0.88692 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3692347 rs36099109 0.149 CREBBP T T 0.04 1.04081 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3692347 rs36099109 0.409 CREBBP T T 0.02 1.0202 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3694911 rs79213162 0.038 CREBBP C C 0.07 1.07251 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3694911 rs79213162 0.124 CREBBP C C 0.06 1.06184 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3694911 rs79213162 0.149 CREBBP C C -0.07 0.932394 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3694911 rs79213162 0.303 CREBBP C C 0.06 1.06184 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3695272 rs75712687 0.021 CREBBP A A 0.09 1.09417 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3695272 rs75712687 0.106 CREBBP A A -0.1 0.904837 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3695272 rs75712687 0.212 CREBBP A A 0.04 1.04081 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3695272 rs75712687 0.52 CREBBP A A 0.02 1.0202 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3695882 rs75987714 0.042 CREBBP G G 0.1 1.10517 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3695882 rs75987714 0.113 CREBBP G G 0.07 1.07251 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3695882 rs75987714 0.585 CREBBP G G 0.03 1.03045 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3695882 rs75987714 0.734 CREBBP G G -0.02 0.980199 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3696240 rs6500550 0.018 CREBBP T T -0.11 0.895834 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3696240 rs6500550 0.068 CREBBP T T 0.04 1.04081 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3696240 rs6500550 0.121 CREBBP T T 0.05 1.05127 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3696240 rs6500550 0.931 CREBBP T T 0.01 1.01005 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3697203 rs1639150 0.044 CREBBP C C 0.05 1.05127 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3697203 rs1639150 0.046 CREBBP C C 0.06 1.06184 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3697203 rs1639150 0.729 CREBBP C C 0.01 1.01005 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3697203 rs1639150 0.876 CREBBP C C 0 1 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3698678 rs112455953 0.001 CREBBP T T 0.11 1.11628 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3698678 rs112455953 0.059 CREBBP T T 0.06 1.06184 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3698678 rs112455953 0.063 CREBBP T T -0.12 0.88692 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3698678 rs112455953 0.493 CREBBP T T 0.02 1.0202 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3698760 rs112193373 0.002 CREBBP A A 0.11 1.11628 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3698760 rs112193373 0.044 CREBBP A A -0.13 0.878095 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3698760 rs112193373 0.107 CREBBP A A 0.05 1.05127 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3698760 rs112193373 0.493 CREBBP A A 0.02 1.0202 TRAP1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3723163 rs39733 0.015 CREBBP T T 0.12 1.1275 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive downstream_gene_variant chr16 3723163 rs39733 0.081 CREBBP T T 0.11 1.11628 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive downstream_gene_variant chr16 3723163 rs39733 0.16 CREBBP T T 0.03 1.03045 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive downstream_gene_variant chr16 3723163 rs39733 0.848 CREBBP T T 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive downstream_gene_variant chr16 3723489 rs7199513 0.019 CREBBP G G 0.06 1.06184 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive downstream_gene_variant chr16 3723489 rs7199513 0.02 CREBBP G G 0.01 1.01005 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive downstream_gene_variant chr16 3723489 rs7199513 0.223 CREBBP G G 0.04 1.04081 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive downstream_gene_variant chr16 3723489 rs7199513 0.369 CREBBP G G 0.03 1.03045 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive downstream_gene_variant chr16 3784315 rs130024 0.038 CREBBP T T 0.15 1.16183 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3784315 rs130024 0.141 CREBBP T T 0.14 1.15027 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3784315 rs130024 0.463 CREBBP T T -0.04 0.960789 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3784315 rs130024 0.815 CREBBP T T 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3814501 rs7198381 0.001 CREBBP A A 0.19 1.20925 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3814501 rs7198381 0.03 CREBBP A A 0.14 1.15027 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3814501 rs7198381 0.072 CREBBP A A 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3840292 rs62039107 0.019 CREBBP G G 0.12 1.1275 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3840292 rs62039107 0.244 CREBBP G G 0.03 1.03045 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3840292 rs62039107 0.782 CREBBP G G 0.01 1.01005 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3840292 rs62039107 0.95 CREBBP G G 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3867530 rs2526690 0.00037 CREBBP G G 0.2 1.2214 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr16 3867530 rs2526690 0.018 CREBBP G G 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3867530 rs2526690 0.033 CREBBP G G 0.13 1.13883 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr16 3867530 rs2526690 0.732 CREBBP G G -0.09 0.913931 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr16 3888601 rs2386817 0.01 CREBBP A A 0.13 1.13883 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intergenic_region chr16 3888601 rs2386817 0.046 CREBBP A A 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3888601 rs2386817 0.173 CREBBP A A 0.07 1.07251 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3889456 rs58670576 0.018 CREBBP C C 0.15 1.16183 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intergenic_region chr16 3889456 rs58670576 0.028 CREBBP C C 0.15 1.16183 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3889456 rs58670576 0.428 CREBBP C C 0.08 1.08329 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3901739 rs72760840 0.006 CREBBP A A 0.15 1.16183 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3901739 rs72760840 0.119 CREBBP A A 0.04 1.04081 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intergenic_region chr16 3901739 rs72760840 1 CREBBP A A 0.01 1.01005 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3906073 rs2080248 0.022 CREBBP G G 0.13 1.13883 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intergenic_region chr16 3906073 rs2080248 0.032 CREBBP G G 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3906073 rs2080248 0.553 CREBBP G G 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3909436 rs73503973 0.015 CREBBP C C 0.17 1.1853 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intergenic_region chr16 3909436 rs73503973 0.018 CREBBP C C 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3909436 rs73503973 0.451 CREBBP C C 0 1 CREBBP SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3921680 rs117150760 0.033 CREBBP C C 0.14 1.15027 ADCY9 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 3921680 rs117150760 0.121 CREBBP C C 0.09 1.09417 ADCY9 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intergenic_region chr16 3921680 rs117150760 0.618 CREBBP C C -0.08 0.923116 ADCY9 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intergenic_region chr16 10948382 rs8055533 0.0000985 CLEC16A G G NR NA CLEC16A SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD intron_variant chr16 10948382 rs8055533 0.00036 CLEC16A G G NR NA CLEC16A SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 16559 All Type 1 diabetes (T1D) Non-ADRD intron_variant chr16 12967754 rs7192086 0.26 SHISA9 NR NR 0.94 0.94 SHISA9 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr16 12967754 rs7192086 0.74 SHISA9 NR NR 1.03 1.03 SHISA9 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr16 13221798 rs407146 0.0006 LOC729993 T T NR NA SHISA9 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr16 13221798 rs407146 0.0007 LOC729993 T T NR NA SHISA9 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr16 13221798 rs407146 0.0137 LOC729993 T T NR NA SHISA9 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr16 14286074 rs246174 0.000591 MKL2 T T NR NA MRTFB SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intergenic_region chr16 14286074 rs246174 0.000789 MKL2 T T NR NA MRTFB SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr16 14286074 rs246174 0.00441 MKL2 T T 1.04 1.04 MRTFB SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr16 14286074 rs246174 0.00823 MKL2 T T 1.04 1.04 MRTFB SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr16 14286074 rs246174 0.704 MKL2 T T 0.98 0.98 MRTFB SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr16 14286074 rs246174 0.88 MKL2 T T 1 1 MRTFB SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr16 19796841 rs7185636 0.000000024 IQCK C C 0.92 0.92 IQCK SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD intron_variant chr16 19796841 rs7185636 0.000000084 IQCK C C 0.92 0.92 IQCK SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr16 19796841 rs7185636 0.11 IQCK C C 0.94 0.94 IQCK SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD intron_variant chr16 19905573 rs9941245 0.0000258 GPRC5B G G 0.93 0.93 GPRC5B SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr16 19905573 rs9941245 0.0000942 GPRC5B G G 0.94 0.94 GPRC5B SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr16 19905573 rs9941245 0.000229 GPRC5B G G NR NA GPRC5B SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr16 19905573 rs9941245 0.0904 GPRC5B G G 0.9 0.9 GPRC5B SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr16 19905573 rs9941245 0.854 GPRC5B G G 1 1 GPRC5B SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr16 19905573 rs9941245 5.27E-16 GPRC5B G G NR NA GPRC5B SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intergenic_region chr16 19922278 rs12444979 0.001 NR C C 1.105 1.105 GPRC5B SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr16 19922278 rs12444979 0.088 NR C C 1.116 1.116 GPRC5B SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr16 19922278 rs12444979 0.301 NR C C 0.005 1.00501 GPRC5B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr16 19922278 rs12444979 0.981 NR C C 0.999 0.999 GPRC5B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr16 20353266 rs4293393 2.48E-28 UMOD NR NR -0.15 0.860708 UMOD SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma THP Fluid biomarker intron_variant chr16 23355101 rs152745 0.286 SCNN1B NR NR NR NA SCNN1B SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr16 24496796 rs11649538 0.267 RBBP6 NR NR NR NA RBBP6 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology upstream_gene_variant chr16 28874338 rs7359397 0.026 NR T T 0.007 1.00702 SH2B1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive upstream_gene_variant chr16 28874338 rs7359397 0.18 NR T T 0.942 0.942 SH2B1 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD upstream_gene_variant chr16 28874338 rs7359397 0.408 NR T T 1.03 1.03 SH2B1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD upstream_gene_variant chr16 28874338 rs7359397 0.762 NR T T 0.993 0.993 SH2B1 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD upstream_gene_variant chr16 31111250 rs889555 0.000000032 NR T T 0.95 0.95 BCKDK SNP-based Disease risk 29777097 Caucasian UKBB 623001 All AD AD intron_variant chr16 31121779 rs59735493 0.00000372 KAT8 A A NR NA KAT8 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr16 31121779 rs59735493 0.000825 KAT8 A A NR NA KAT8 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr16 31121779 rs59735493 3.98E-08 KAT8 A A -5.49 NA KAT8 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr16 48598567 rs11649236 1.20E-26 N4BP1 NR NR -1.48 0.227638 N4BP1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD N4BP1 expression in Cerebellar Expression intron_variant chr16 48598567 rs11649236 2.53E-63 N4BP1 NR NR -1.57 0.208045 N4BP1 SNP-based eQTL 22685416 Caucasian MAYO 374 All N4BP1 expression in Cerebellar Expression intron_variant chr16 48598567 rs11649236 5.25E-82 N4BP1 NR NR -1.44 0.236928 N4BP1 SNP-based eQTL 22685416 Caucasian MAYO 399 All N4BP1 expression in Temporal cortex Expression intron_variant chr16 48598567 rs11649236 8.82E-34 N4BP1 NR NR -1.7 0.182684 N4BP1 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD N4BP1 expression in Cerebellar Expression intron_variant chr16 53766842 rs9940128 0.000000011 FTO NR NR NR NA FTO SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr16 53769662 rs1558902 0.313 NR A A 0.961 0.961 FTO SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr16 53769662 rs1558902 0.568 NR A A 0 1 FTO SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr16 53769662 rs1558902 0.905 NR A A 0.996 0.996 FTO SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr16 53778702 rs8057044 0.000000027 FTO NR NR NR NA FTO SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr16 53796553 rs9930506 2.80E-09 FTO NR NR NR NA FTO SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr16 54121830 rs16953089 0.000136 FTO C C NR NA FTO SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr16 54121830 rs16953089 0.000862 FTO C C NR NA FTO SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD 3_prime_UTR_variant chr16 54121830 rs16953089 0.000985 FTO C C 0.95 0.95 FTO SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD 3_prime_UTR_variant chr16 54121830 rs16953089 0.00463 FTO C C 0.96 0.96 FTO SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD 3_prime_UTR_variant chr16 54121830 rs16953089 0.184 FTO C C 1.07 1.07 FTO SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD 3_prime_UTR_variant chr16 54121830 rs16953089 0.654 FTO C C 1 1 FTO SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD 3_prime_UTR_variant chr16 56464599 rs4784670 0.0764 OGFOD1 NR NR NR NA OGFOD1 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr16 58107923 rs74019790 0.0005 C16orf80 T T NR NA CFAP20 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr16 58107923 rs74019790 6.30E-09 NR T T NR NA CFAP20 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group C16orf80 (ENSG00000070761) expression Expression intergenic_region chr16 59856794 rs8056650 0.00000147 NR A A -302.5 4.2259e-132 GOT2 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intron_variant chr16 59856794 rs8056650 0.0000317 NR A A -302.5 4.2259e-132 GOT2 SNP-based Endophenotype 20197096 Caucasian ADNI 698 All Hippocampal Volume Imaging intron_variant chr16 66110270 rs12595955 0.000469 CDH5 G G NR NA CDH5 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intergenic_region chr16 66110270 rs12595955 0.00174 CDH5 G G NR NA CDH5 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr16 66110270 rs12595955 0.966 CDH5 G G 1 1 CDH5 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr16 70081616 rs998109 0.0000164 PDXDC2 NR NR NR NA PDPR SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD upstream_gene_variant chr16 70660097 rs4985556 0.00000141 IL34 A A 1.11 1.11 IL34 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD synonymous_variant chr16 70660097 rs4985556 0.00000206 IL34 A A 1.1 1.1 IL34 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD synonymous_variant chr16 70660097 rs4985556 0.000211 IL34 A A NR NA IL34 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD synonymous_variant chr16 70660097 rs4985556 0.00041 IL34 A A NR NA IL34 SNP-based Cross phenotype 30413934 Caucasian DIAGRAM 298939 All Type 2 diabetes (T2D) Non-ADRD synonymous_variant chr16 70660097 rs4985556 0.00355 IL34 A A 1.01 1.01 IL34 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD synonymous_variant chr16 70660097 rs4985556 0.748 IL34 A A 1.03 1.03 IL34 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD synonymous_variant chr16 70671071 rs4985557 0.0000287 MTSS1L T T NR NA MTSS2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr16 70671071 rs4985557 0.0000334 MTSS1L T T 1.06 1.06 MTSS2 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr16 70671071 rs4985557 0.0000928 MTSS1L T T 1.05 1.05 MTSS2 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr16 70671071 rs4985557 0.000119 MTSS1L T T NR NA MTSS2 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr16 70671071 rs4985557 0.139 MTSS1L T T 1.08 1.08 MTSS2 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr16 70671071 rs4985557 0.693 MTSS1L T T 1 1 MTSS2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr16 70702849 rs11649476 0.0000135 VAC14 T T NR NA VAC14 SNP-based Cross phenotype 30930738 Caucasian IGAP 54162 All AD AD intron_variant chr16 70702849 rs11649476 0.0000298 VAC14 T T NR NA VAC14 SNP-based Cross phenotype 30930738 Caucasian PGC2-BIP 51710 All Bipolar disorder (BIP) ADRD intron_variant chr16 71398604 rs12373108 0.000000502 "CALB2, ZNF23" T T 1.21 1.21 CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 19025 All Brain infarcts (BI) Imaging intergenic_region chr16 71398604 rs12373108 0.000014 "CALB2, ZNF23" T T 1.23 1.23 CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 14645 All Small sub-cortical brain infarcts (SSBI) Imaging intergenic_region chr16 71398604 rs12373108 0.0000153 "CALB2, ZNF23" T T NR NA CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 19025 All Brain infarcts (BI) Imaging intergenic_region chr16 71398604 rs12373108 0.0000899 "CALB2, ZNF23" NR NR 1.12 1.12 CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 25887 All Brain infarcts (BI) Imaging intergenic_region chr16 71398604 rs12373108 0.000137 "CALB2, ZNF23" T T NR NA CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 14645 All Small sub-cortical brain infarcts (SSBI) Imaging intergenic_region chr16 71398604 rs12373108 0.00022 "CALB2, ZNF23" NR NR 1.13 1.13 CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 21507 All Small sub-cortical brain infarcts (SSBI) Imaging intergenic_region chr16 71398604 rs12373108 0.28 "CALB2, ZNF23" NR NR 1.04 1.04 CALB2 SNP-based Endophenotype 30651383 Caucasian "METASTROKE, SiGN, YLSDR" 41039 All Ischemic stroke due to small vessel disease (IS-SVD) Imaging intergenic_region chr16 71398604 rs12373108 0.34 "CALB2, ZNF23" NR NR 1.05 1.05 CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Small sub-cortical brain infarcts (SSBI) Imaging intergenic_region chr16 71398604 rs12373108 0.44 "CALB2, ZNF23" NR NR 0.94 0.94 CALB2 SNP-based Endophenotype 30651383 Caucasian ADGC 2940 All Pathologically defined infarcts Imaging intergenic_region chr16 71398604 rs12373108 0.73 "CALB2, ZNF23" NR NR 1.01 1.01 CALB2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Brain infarcts (BI) Imaging intergenic_region chr16 71398604 rs12373108 0.87 "CALB2, ZNF23" NR NR 1 1 CALB2 SNP-based Endophenotype 30651383 Caucasian "CHARGE, METASTROKE, SiGN" 137560 All Ischemic stroke (IS) Imaging intergenic_region chr16 72014733 rs8062895 0.000412 DHODH G G NR NA DHODH SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr16 72014733 rs8062895 0.00156 DHODH G G NR NA DHODH SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr16 72014733 rs8062895 0.181 DHODH G G 1 1 DHODH SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr16 73703474 rs7184882 0.000000664 LOC101927998 T T 0.71 0.71 ZFHX3 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intergenic_region chr16 73703474 rs7184882 0.00000308 LOC101927998 T T 0.78 0.78 ZFHX3 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intergenic_region chr16 73703474 rs7184882 0.08 LOC101927998 T T 0.89 0.89 ZFHX3 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intergenic_region chr16 75212521 rs9927309 0.000009 BCAR1 NR NR NR NA CTRB2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr16 78197597 rs55751884 0.00000919 WWOX C C NR NA WWOX SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intron_variant chr16 79321960 rs62039712 0.000000037 WWOX A A 1.16 1.16 WWOX SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD intergenic_region chr16 79321960 rs62039712 0.00000012 WWOX A A 1.17 1.17 WWOX SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intergenic_region chr16 79321960 rs62039712 0.13 WWOX A A 1.14 1.14 WWOX SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 30511 All Clinically diagnosed LOAD AD intergenic_region chr16 79648854 rs1424233 0.312 NR A A 0.978 0.978 MAF SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr16 79648854 rs1424233 0.669 NR A A 0 1 MAF SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr16 79648854 rs1424233 0.764 NR A A 0.987 0.987 MAF SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr16 79648854 rs1424233 0.936 NR A A 1 1 MAF SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr16 81738931 rs9931998 0.000459 BC040927 A A 0.94 0.94 PLCG2 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr16 81738931 rs9931998 0.000523 BC040927 A A NR NA PLCG2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr16 81738931 rs9931998 0.00112 BC040927 A A 0.95 0.95 PLCG2 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr16 81738931 rs9931998 0.00199 BC040927 A A NR NA PLCG2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr16 81738931 rs9931998 0.589 BC040927 A A 1.04 1.04 PLCG2 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr16 81908423 rs72824905 0.0000119 PLCG2 G G 0.65 0.65 PLCG2 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 33786 All AD AD missense_variant chr16 81908423 rs72824905 0.000135 PLCG2 G G 0.7 0.7 PLCG2 SNP-based Disease risk 28714976 Caucasian "CHARGE, EADI, GERAD" 35831 All AD AD missense_variant chr16 81908423 rs72824905 0.0248 PLCG2 G G 0.69 0.69 PLCG2 SNP-based Disease risk 28714976 Caucasian ADGC 15288 All AD AD missense_variant chr16 81908423 rs72824905 5.38E-10 PLCG2 G G 0.68 0.68 PLCG2 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 84905 All AD AD missense_variant chr16 86243835 rs4843359 0.00000581 NR NR NR NR NA FOXF1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr16 86243835 rs4843359 0.000122 NR NR NR 2.19 2.19 FOXF1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr16 86243835 rs4843359 0.000277 NR NR NR NR NA FOXF1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr16 86243835 rs4843359 0.00636 NR NR NR 1.69 1.69 FOXF1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr16 86243835 rs4843359 0.09346 NR NR NR NR NA FOXF1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr16 86243835 rs4843359 0.39124 NR NR NR NR NA FOXF1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr16 86243835 rs4843359 0.78 NR NR NR NR NA FOXF1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr16 86243835 rs4843359 0.887 NR NR NR NR NA FOXF1 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr16 86243835 rs4843359 1 NR NR NR 0.93 0.93 FOXF1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr16 86340602 rs2581305 0.000000398 LINC00917 NR NR 0.608 1.83675 FOXF1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr16 86340602 rs2581305 0.000403 LINC00917 NR NR 0.577 1.78069 FOXF1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr16 86340602 rs2581305 0.000583 LINC00917 NR NR 0.615 1.84966 FOXF1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr16 86547585 rs8047645 0.0238 MTHFSD A A NR NA MTHFSD SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr16 86547585 rs8047645 7.35E-45 NR A A NR NA MTHFSD SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group MTHFSD (ILMN_1797046) expression Expression intron_variant chr16 87078024 rs12933233 0.00000764 NR NR NR NR NA C16orf95 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intergenic_region chr16 87078024 rs12933233 0.0000199 NR NR NR NR NA C16orf95 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intergenic_region chr16 87078024 rs12933233 0.000563 NR NR NR 0.91 2.48432 C16orf95 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intergenic_region chr16 87078024 rs12933233 0.00846 NR NR NR 0.79 2.2034 C16orf95 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intergenic_region chr16 87078024 rs12933233 0.135 NR NR NR 2.92 18.5413 C16orf95 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intergenic_region chr17 4863642 rs8070572 0.000000198 MINK1 C C 1.12 1.12 MINK1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr17 4863642 rs8070572 0.00000149 MINK1 C C 1.11 1.11 MINK1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr17 4863642 rs8070572 0.00000492 MINK1 C C NR NA MINK1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr17 4863642 rs8070572 0.000624 MINK1 C C NR NA MINK1 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr17 4863642 rs8070572 0.00638 MINK1 C C 1.01 1.01 MINK1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr17 4863642 rs8070572 0.0305 MINK1 C C 1.2 1.2 MINK1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr17 5081152 rs9916042 4.73E-08 SCIMP A A NR NA ZFP3 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr17 5233752 rs7225151 0.448 SCIMP A A 0.952 0.952 SCIMP SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr17 5235685 rs113260531 0.00000321 SCIMP A A NR NA SCIMP SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr17 5235685 rs113260531 9.16E-10 SCIMP A A 6.12 NA SCIMP SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr17 7288772 rs222842 0.201 SLC24A4 (to be removed) G G 1.09 NA YBX2 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other 3_prime_UTR_variant chr17 7383007 rs1554948 0.000063 TNK1 NR NR 1.19 1.19 TNK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD synonymous_variant chr17 7383007 rs1554948 0.009 TNK1 NR NR NR NA TNK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD synonymous_variant chr17 7383007 rs1554948 0.021 TNK1 NR NR NR NA TNK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD synonymous_variant chr17 7383007 rs1554948 0.054 TNK1 NR NR NR NA TNK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD synonymous_variant chr17 7383007 rs1554948 0.13 TNK1 NR NR NR NA TNK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD synonymous_variant chr17 7383007 rs1554948 0.569 TNK1 A A 0.96 0.96 TNK1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD synonymous_variant chr17 7383007 rs1554948 0.699 TNK1 NR NR NR NA TNK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD synonymous_variant chr17 10320397 rs2074877 0.00072 MYH13 NR NR 1.12 1.12 MYH13 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD missense_variant chr17 10320397 rs2074877 0.017 MYH13 NR NR NR NA MYH13 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD missense_variant chr17 10320397 rs2074877 0.029 MYH13 NR NR NR NA MYH13 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD missense_variant chr17 10320397 rs2074877 0.664 MYH13 NR NR NR NA MYH13 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD missense_variant chr17 10320397 rs2074877 0.742 MYH13 NR NR NR NA MYH13 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD missense_variant chr17 10320397 rs2074877 0.931 MYH13 NR NR NR NA MYH13 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD missense_variant chr17 18758014 rs12603319 0.39 FBXW10 T T NR NA FBXW10 SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intron_variant chr17 18758014 rs12603319 1.14E-08 FBXW10 T T NR NA FBXW10 SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intron_variant chr17 19656155 rs962800 1.14E-72 ALDH3A2 NR NR 0.44 1.55271 ALDH3A2 SNP-based eQTL 22685416 Caucasian MAYO 399 All ALDH3A2 expression in Temporal cortex Expression intron_variant chr17 19656155 rs962800 1.47E-58 ALDH3A2 NR NR 0.46 1.58407 ALDH3A2 SNP-based eQTL 22685416 Caucasian MAYO 374 All ALDH3A2 expression in Cerebellar Expression intron_variant chr17 19656155 rs962800 2.05E-32 ALDH3A2 NR NR 0.49 1.63232 ALDH3A2 SNP-based eQTL 22685416 Caucasian MAYO 197 AD ALDH3A2 expression in Cerebellar Expression intron_variant chr17 19656155 rs962800 3.48E-22 ALDH3A2 NR NR 0.44 1.55271 ALDH3A2 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD ALDH3A2 expression in Cerebellar Expression intron_variant chr17 27757506 rs11653716 0.00014 NOS2A NR NR NR NA NOS2 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr17 27757506 rs11653716 0.00353 NOS2A NR NR NR NA NOS2 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr17 27757506 rs11653716 0.00725 NOS2A NR NR NR NA NOS2 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr17 31378929 rs2525574 1.22E-85 EVI2A NR NR 1.67 5.31217 NF1 SNP-based eQTL 22685416 Caucasian MAYO 399 All EVI2A expression in Temporal cortex Expression stop_lost chr17 31378929 rs2525574 3.92E-43 EVI2A NR NR 1.79 5.98945 NF1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD EVI2A expression in Cerebellar Expression stop_lost chr17 31378929 rs2525574 6.73E-94 EVI2A NR NR 1.81 6.11045 NF1 SNP-based eQTL 22685416 Caucasian MAYO 374 All EVI2A expression in Cerebellar Expression stop_lost chr17 31378929 rs2525574 9.05E-43 EVI2A NR NR 1.81 6.11045 NF1 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD EVI2A expression in Cerebellar Expression stop_lost chr17 34333130 rs12602195 2.40E-12 CCL8 NR NR -0.08 0.923116 CCL8 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma MCP-2 Fluid biomarker upstream_gene_variant chr17 35960396 rs4795104 1.02E-17 CCL16 T T NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker downstream_gene_variant chr17 35960396 rs4795104 9.63E-16 CCL16 T T NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker downstream_gene_variant chr17 35965995 rs4796144 1.02E-17 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker upstream_gene_variant chr17 35965995 rs4796144 9.63E-16 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker upstream_gene_variant chr17 35968241 rs149197550 8.32E-16 CCL16 T T NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker upstream_gene_variant chr17 35968241 rs149197550 9.20E-18 CCL16 T T NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker upstream_gene_variant chr17 35976276 rs80329614 1.67E-19 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker downstream_gene_variant chr17 35976276 rs80329614 5.85E-28 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker downstream_gene_variant chr17 35976735 rs33995560 2.09E-27 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker 3_prime_UTR_variant chr17 35976735 rs33995560 2.94E-19 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker 3_prime_UTR_variant chr17 35977228 rs150951362 1.65E-17 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker 3_prime_UTR_variant chr17 35977228 rs150951362 2.05E-20 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker 3_prime_UTR_variant chr17 35978012 rs7216969 2.09E-27 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker intron_variant chr17 35978012 rs7216969 2.94E-19 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker intron_variant chr17 35978035 rs11080368 1.78E-27 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker intron_variant chr17 35978035 rs11080368 2.32E-19 CCL16 A A NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker intron_variant chr17 35978128 rs11080369 0.00101 CCL16 NR NR -2.41 0.0898153 CCL16 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma HCC-4 Fluid biomarker intron_variant chr17 35978128 rs11080369 1.78E-27 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker intron_variant chr17 35978128 rs11080369 2.32E-19 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker intron_variant chr17 35978128 rs11080369 8.03E-19 CCL16 NR NR -0.22 0.802519 CCL16 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma HCC-4 Fluid biomarker intron_variant chr17 35979434 rs75236781 2.96E-17 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 543 All CSF CCL16 Fluid biomarker intron_variant chr17 35979434 rs75236781 3.94E-20 CCL16 C C NR NA CCL16 SNP-based Cross phenotype 27357396 Caucasian "ADNI, Knight-ADRC" 587 All Plasma CCL16 Fluid biomarker intron_variant chr17 36018624 rs854656 2.61E-13 CCL23 NR NR -0.07 0.932394 CCL23 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma MPIF-1 Fluid biomarker upstream_gene_variant chr17 36058726 rs854462 0.0000867 CCL18 NR NR 61.74 650640829100921095358251008 CCL18 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma PARC Fluid biomarker intergenic_region chr17 36058726 rs854462 9.15E-24 CCL18 NR NR 0.15 1.16183 CCL18 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma PARC Fluid biomarker intergenic_region chr17 36817647 rs8070114 0.00000358 LHX1 A A 0.68 0.68 LHX1 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intergenic_region chr17 36819274 rs1497197 0.00000296 LHX1 A A 0.67 0.67 LHX1 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intergenic_region chr17 37738049 rs4430796 0.0000024 HNF1B NR NR NR NA HNF1B SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr17 38784819 rs12952045 0.037 CWC25 T T NR NA PIP4K2B SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr17 38784819 rs12952045 9.63E-44 NR T T NR NA PIP4K2B SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group CWC25 (ILMN_1720233) expression Expression intron_variant chr17 40004501 rs8070454 1.06E-81 MED24 NR NR -2.16 0.115325 PSMD3 SNP-based eQTL 22685416 Caucasian MAYO 399 All MED24 expression in Temporal cortex Expression intergenic_region chr17 40004501 rs8070454 1.56E-74 MED24 NR NR -2.03 0.131336 PSMD3 SNP-based eQTL 22685416 Caucasian MAYO 374 All MED24 expression in Cerebellar Expression intergenic_region chr17 40004501 rs8070454 3.15E-40 MED24 NR NR -2.05 0.128735 PSMD3 SNP-based eQTL 22685416 Caucasian MAYO 197 AD MED24 expression in Cerebellar Expression intergenic_region chr17 40004501 rs8070454 7.82E-28 MED24 NR NR -1.98 0.138069 PSMD3 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD MED24 expression in Cerebellar Expression intergenic_region chr17 40075600 rs939348 0.757 THRA T T 0.97 0.97 THRA SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr17 40597298 rs11658260 0.665 SMARCE1 A A 0.97 0.97 SMARCE1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr17 44343224 rs72824731 0.0021 GRN C C 3.88 3.88 GRN SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (REC Model) Hippocampal sclerosis of aging ADRD upstream_gene_variant chr17 44346188 rs2879096 0.014 GRN NR NR 1.38 1.38 GRN SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (DOM Model) Hippocampal sclerosis of aging ADRD 5_prime_UTR_variant chr17 44346188 rs2879096 0.032 GRN T T 1.25 1.25 GRN SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (ADD Model) Hippocampal sclerosis of aging ADRD 5_prime_UTR_variant chr17 44352876 rs5848 0.073 GRN T T 1.9 1.9 GRN SNP-based Disease risk 24770881 Caucasian ADGC 176 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 0.218 GRN T T 1.16 1.16 GRN SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 0.541 GRN T T 1.08 1.08 GRN SNP-based Disease risk 24770881 Caucasian ADGC 1636 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 0.774 GRN T T 1.12 1.12 GRN SNP-based Disease risk 24770881 Caucasian ADGC 427 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 NR ABCC9 T T 1.25 1.25 GRN SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 NR ABCC9 T T 1.33 1.33 GRN SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 NR ABCC9 T T 1.35 1.35 GRN SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 NR ABCC9 T T 1.74 1.74 GRN SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 NR ABCC9 T T 1.92 1.92 GRN SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 44352876 rs5848 NR ABCC9 T T 2.24 2.24 GRN SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD 3_prime_UTR_variant chr17 45641777 rs393152 0.000117 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intron_variant chr17 45641777 rs393152 2.22E-18 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intron_variant chr17 45641777 rs393152 NR MAPT A A 2.18 2.18 LINC02210-CRHR1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr17 45641777 rs393152 NR ZCWPW1 A A 1.77 1.77 LINC02210-CRHR1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr17 45641777 rs393152 NR ZCWPW1 A A 3.73 3.73 LINC02210-CRHR1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr17 45725823 rs1358071 0.000000027 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Medulla Expression intron_variant chr17 45725823 rs1358071 0.000000491 CRHR1 A A 1.19 1.19 LINC02210-CRHR1 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr17 45725823 rs1358071 0.00000061 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All KANSL1 expression in Hippocampus Expression intron_variant chr17 45725823 rs1358071 0.0000022 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Putamen Expression intron_variant chr17 45725823 rs1358071 0.0000029 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All CRHR1 expression in Medulla Expression intron_variant chr17 45725823 rs1358071 0.0000077 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in White matter Expression intron_variant chr17 45725823 rs1358071 0.0000496 CRHR1 A A 1.22 1.22 LINC02210-CRHR1 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intron_variant chr17 45725823 rs1358071 0.0000496 CRHR1 NR NR NR NA LINC02210-CRHR1 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr17 45725823 rs1358071 0.001 CRHR1 A A 1.16 1.16 LINC02210-CRHR1 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intron_variant chr17 45725823 rs1358071 1.90E-11 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Occipital cortex Expression intron_variant chr17 45725823 rs1358071 3.10E-12 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Temporal cortex Expression intron_variant chr17 45725823 rs1358071 3.60E-10 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Frontal cortex Expression intron_variant chr17 45725823 rs1358071 4.70E-10 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Hippocampus Expression intron_variant chr17 45725823 rs1358071 5.70E-12 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Thalamus Expression intron_variant chr17 45725823 rs1358071 7.30E-11 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Substantia nigra Expression intron_variant chr17 45725823 rs1358071 7.40E-22 CRHR1 A A NR NA LINC02210-CRHR1 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A4 expression in Cerebellum Expression intron_variant chr17 45900461 rs1864325 0.03 MAPT T T 0.81 0.81 MAPT SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1352 All Age of AD onset Other intron_variant chr17 45900461 rs1864325 0.22 MAPT T T 0.81 0.81 MAPT SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1352 All AD AD intron_variant chr17 45908813 rs1467967 0.0000093 MAPT NR NR 0.16 1.17351 MAPT SNP-based eQTL 25324900 Caucasian MAYO 166 All MAPT(ILMN_1710903) expression in temporal cortex Expression intron_variant chr17 45908813 rs1467967 0.00026 MAPT NR NR 0.15 1.16183 MAPT SNP-based eQTL 25324900 Caucasian MAYO 171 All MAPT(ILMN_1710903) expression in Cerebellum Expression intron_variant chr17 45908813 rs1467967 0.011 MAPT NR NR 0.11 1.11628 MAPT SNP-based eQTL 25324900 Caucasian MAYO 166 All MAPT (ILMN_2298727) expressionin temporal cortex Expression intron_variant chr17 45908813 rs1467967 0.019 MAPT NR NR 0.12 1.1275 MAPT SNP-based eQTL 25324900 Caucasian MAYO 171 All MAPT (ILMN_2298727) expressionin Cerebellum Expression intron_variant chr17 45908813 rs1467967 0.062 MAPT G G 1.05 1.05 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 19351 All LOAD Risk AD intron_variant chr17 45908813 rs1467967 0.079 MAPT G G 1.1 1.1 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 4986 All LOAD Risk AD intron_variant chr17 45908813 rs1467967 0.102 MAPT G G 1.05 1.05 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 14365 All LOAD Risk AD intron_variant chr17 45908813 rs1467967 0.604 MAPT NR NR -0.01 0.99005 MAPT SNP-based eQTL 25324900 Caucasian MAYO 171 All MAPT (ILMN_2310814) expression in Cerebellum Expression intron_variant chr17 45908813 rs1467967 0.859 MAPT NR NR 0 1 MAPT SNP-based eQTL 25324900 Caucasian MAYO 166 All MAPT (ILMN_2310814) expression in temporal cortex Expression intron_variant chr17 45942346 rs242557 0.000000011 MAPT NR NR 0.18 1.19722 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All MAPT (ILMN_1710903) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.000000034 MAPT NR NR 0.23 1.2586 MAPT SNP-based eQTL 25324900 Caucasian MAYO 180 All MAPT(ILMN_1710903) expression in Cerebellum Expression intron_variant chr17 45942346 rs242557 0.00000239 MAPT NR NR 0.18 1.19722 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAPT (ILMN_1710903) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.000012 MAPT NR NR 0.17 1.1853 MAPT SNP-based eQTL 25324900 Caucasian MAYO 173 All MAPT(ILMN_1710903) expression in temporal cortex Expression intron_variant chr17 45942346 rs242557 0.00978 MAPT NR NR 0.07 1.07251 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All MAPT (ILMN_2298727) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.0166 MAPT NR NR 0.09 1.09417 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MAPT (ILMN_1710903) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.0226 MAPT NR NR 0.11 1.11628 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD MAPT (ILMN_2298727) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.05 MAPT NR NR 0.1 1.10517 MAPT SNP-based eQTL 25324900 Caucasian MAYO 180 All MAPT (ILMN_2298727) expressionin Cerebellum Expression intron_variant chr17 45942346 rs242557 0.0659 STH NR NR -0.03 0.970446 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All STH (ILMN_1665311) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.0856 MAPT NR NR 0.08 1.08329 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAPT (ILMN_2298727) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.091 MAPT NR NR 0.08 1.08329 MAPT SNP-based eQTL 25324900 Caucasian MAYO 173 All MAPT (ILMN_2298727) expressionin temporal cortex Expression intron_variant chr17 45942346 rs242557 0.0913 MAPT NR NR -0.03 0.970446 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MAPT (ILMN_2310814) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.0933 MAPT NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD MAPT (ILMN_2310814) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.094 MAPT NR NR 0.09 1.09417 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MAPT (ILMN_2298727) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.109 MAPT NR NR -0.03 0.970446 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All MAPT (ILMN_2310814) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.15 KIAA1267 NR NR 0.03 1.03045 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP KIAA1267 (ILMN_2200636) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.196 MAPT NR NR -0.02 0.980199 MAPT SNP-based eQTL 25324900 Caucasian MAYO 180 All MAPT (ILMN_2310814) expression in Cerebellum Expression intron_variant chr17 45942346 rs242557 0.217 MAPT NR NR 0.04 1.04081 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All MAPT (ILMN_2298727) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.223 KIAA1267 NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD KIAA1267 (ILMN_2200636) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.256 KIAA1267 NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP KIAA1267 (ILMN_2200636) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.259 KIAA1267 NR NR -0.01 0.99005 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All KIAA1267 (ILMN_2200636) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.291 STH NR NR -0.08 0.923116 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP STH (ILMN_1665311) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.349 MAPT NR NR -0.05 0.951229 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MAPT (ILMN_2310814) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.383 KIAA1267 NR NR 0.01 1.01005 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All KIAA1267 (ILMN_2200636) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.426 MAPT NR NR -0.05 0.951229 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MAPT (ILMN_2298727) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.428 STH NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All STH (ILMN_1665311) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.442 STH NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD STH (ILMN_1665311) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.488 STH NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP STH (ILMN_1665311) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.489 STH NR NR 0.03 1.03045 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD STH (ILMN_1665311) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.584 MAPT NR NR 0.01 1.01005 MAPT SNP-based eQTL 25324900 Caucasian MAYO 173 All MAPT (ILMN_2310814) expression in temporal cortex Expression intron_variant chr17 45942346 rs242557 0.619 MAPT NR NR 0.01 1.01005 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAPT (ILMN_2310814) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.665 MAPT NR NR -0.03 0.970446 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MAPT (ILMN_1710903) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.721 MAPT A A 1.01 1.01 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 13407 All LOAD Risk AD intron_variant chr17 45942346 rs242557 0.808 KIAA1267 NR NR 0 1 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD KIAA1267 (ILMN_2200636) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 0.827 MAPT NR NR 0 1 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All MAPT (ILMN_2310814) expression in Cerebellar Expression intron_variant chr17 45942346 rs242557 0.974 MAPT A A 1 1 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 18342 All LOAD Risk AD intron_variant chr17 45942346 rs242557 0.988 MAPT A A 1 1 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 4935 All LOAD Risk AD intron_variant chr17 45942346 rs242557 2.70E-71 MAPT NA NA 0.51 0.51 MAPT SNP-based Disease Risk 22685416 Caucasian "Cohorts from Europe, USA" 8851 All Progressive Supranuclear Palsy (PSP) ADRD intron_variant chr17 45942346 rs242557 4.03E-10 MAPT NR NR 0.25 1.28403 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD MAPT (ILMN_1710903) expression in Temporal cortex Expression intron_variant chr17 45942346 rs242557 8.80E-13 MAPT NR NR 0.18 1.19722 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All MAPT (ILMN_1710903) expression in Cerebellar Expression intron_variant chr17 45977067 rs3785883 0.005 MAPT NR NR 0.14 1.15027 MAPT SNP-based eQTL 25324900 Caucasian MAYO 175 All MAPT(ILMN_1710903) expression in temporal cortex Expression 5_prime_UTR_variant chr17 45977067 rs3785883 0.032 MAPT A A 1.08 1.08 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 15187 All LOAD Risk AD 5_prime_UTR_variant chr17 45977067 rs3785883 0.034 MAPT A A 1.06 1.06 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 20343 All LOAD Risk AD 5_prime_UTR_variant chr17 45977067 rs3785883 0.266 MAPT NR NR -0.07 0.932394 MAPT SNP-based eQTL 25324900 Caucasian MAYO 181 All MAPT (ILMN_2298727) expressionin Cerebellum Expression 5_prime_UTR_variant chr17 45977067 rs3785883 0.274 MAPT A A 1.07 1.07 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 5247 All LOAD Risk AD 5_prime_UTR_variant chr17 45977067 rs3785883 0.548 MAPT NR NR 0.03 1.03045 MAPT SNP-based eQTL 25324900 Caucasian MAYO 181 All MAPT(ILMN_1710903) expression in Cerebellum Expression 5_prime_UTR_variant chr17 45977067 rs3785883 0.621 MAPT NR NR -0.01 0.99005 MAPT SNP-based eQTL 25324900 Caucasian MAYO 175 All MAPT (ILMN_2310814) expression in temporal cortex Expression 5_prime_UTR_variant chr17 45977067 rs3785883 0.706 MAPT NR NR 0.01 1.01005 MAPT SNP-based eQTL 25324900 Caucasian MAYO 181 All MAPT (ILMN_2310814) expression in Cerebellum Expression 5_prime_UTR_variant chr17 45977067 rs3785883 0.977 MAPT NR NR 0 1 MAPT SNP-based eQTL 25324900 Caucasian MAYO 175 All MAPT (ILMN_2298727) expressionin temporal cortex Expression 5_prime_UTR_variant chr17 45979401 rs1981997 1.13E-27 MAPT NR NR -0.44 0.644036 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAPT expression in Cerebellar Expression intron_variant chr17 45979401 rs1981997 1.85E-65 MAPT NR NR -0.48 0.618783 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All MAPT expression in Cerebellar Expression intron_variant chr17 45979401 rs1981997 6.48E-41 MAPT NR NR -0.51 0.600496 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All MAPT expression in Temporal cortex Expression intron_variant chr17 45979401 rs1981997 8.38E-32 MAPT NR NR -0.51 0.600496 MAPT SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD MAPT expression in Cerebellar Expression intron_variant chr17 45998697 rs2471738 0.016 MAPT NR NR 0.11 1.11628 MAPT SNP-based eQTL 25324900 Caucasian MAYO 182 All MAPT(ILMN_1710903) expression in Cerebellum Expression intron_variant chr17 45998697 rs2471738 0.089 MAPT NR NR 0.09 1.09417 MAPT SNP-based eQTL 25324900 Caucasian MAYO 182 All MAPT (ILMN_2298727) expressionin Cerebellum Expression intron_variant chr17 45998697 rs2471738 0.101 MAPT NR NR 0.07 1.07251 MAPT SNP-based eQTL 25324900 Caucasian MAYO 176 All MAPT(ILMN_1710903) expression in temporal cortex Expression intron_variant chr17 45998697 rs2471738 0.109 MAPT T T 1.05 1.05 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 19463 All LOAD Risk AD intron_variant chr17 45998697 rs2471738 0.194 MAPT T T 1.05 1.05 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 14181 All LOAD Risk AD intron_variant chr17 45998697 rs2471738 0.25 MAPT T T 1.07 1.07 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 5282 All LOAD Risk AD intron_variant chr17 45998697 rs2471738 0.386 MAPT NR NR 0.02 1.0202 MAPT SNP-based eQTL 25324900 Caucasian MAYO 176 All MAPT (ILMN_2310814) expression in temporal cortex Expression intron_variant chr17 45998697 rs2471738 0.397 MAPT NR NR -0.01 0.99005 MAPT SNP-based eQTL 25324900 Caucasian MAYO 182 All MAPT (ILMN_2310814) expression in Cerebellum Expression intron_variant chr17 45998697 rs2471738 0.665 MAPT NR NR 0.02 1.0202 MAPT SNP-based eQTL 25324900 Caucasian MAYO 176 All MAPT (ILMN_2298727) expressionin temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.000000336 MAPT NR NR -0.17 0.843665 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All MAPT (ILMN_2298727) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.000053 MAPT G G 0.9 0.9 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 21024 All LOAD Risk AD intron_variant chr17 46003698 rs8070723 0.0000867 MAPT NR NR -0.21 0.810584 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD MAPT (ILMN_2298727) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.00013 MAPT G G 0.89 0.89 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 15895 All LOAD Risk AD intron_variant chr17 46003698 rs8070723 0.00049 MAPT NR NR -0.2 0.818731 MAPT SNP-based eQTL 25324900 Caucasian MAYO 181 All MAPT (ILMN_2298727) expressionin Cerebellum Expression intron_variant chr17 46003698 rs8070723 0.0007 MAPT G G 0.81 0.81 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 5129 All LOAD Risk AD intron_variant chr17 46003698 rs8070723 0.00084 MAPT NR NR -0.16 0.852144 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAPT (ILMN_2298727) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.000903 MAPT NR NR -0.14 0.869358 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All MAPT (ILMN_2298727) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.002 MAPT NR NR -0.16 0.852144 MAPT SNP-based eQTL 25324900 Caucasian MAYO 174 All MAPT (ILMN_2298727) expressionin temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.0179 STH NR NR 0.04 1.04081 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All STH (ILMN_1665311) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.0404 KIAA1267 NR NR 0.04 1.04081 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD KIAA1267 (ILMN_2200636) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.0756 STH NR NR 0.11 1.11628 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP STH (ILMN_1665311) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.0905 MAPT NR NR -0.28 0.755784 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MAPT (ILMN_1710903) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.102 KIAA1267 NR NR -0.03 0.970446 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD KIAA1267 (ILMN_2200636) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.103 MAPT NR NR 0.02 1.0202 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD MAPT (ILMN_2310814) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.114 KIAA1267 NR NR 0.02 1.0202 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All KIAA1267 (ILMN_2200636) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.17 KIAA1267 NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All KIAA1267 (ILMN_2200636) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.186 STH NR NR 0.05 1.05127 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All STH (ILMN_1665311) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.222 MAPT NR NR 0.02 1.0202 MAPT SNP-based eQTL 25324900 Caucasian MAYO 181 All MAPT (ILMN_2310814) expression in Cerebellum Expression intron_variant chr17 46003698 rs8070723 0.259 STH NR NR 0.19 1.20925 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP STH (ILMN_1665311) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.287 KIAA1267 NR NR 0.05 1.05127 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP KIAA1267 (ILMN_2200636) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.305 STH NR NR 0.03 1.03045 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD STH (ILMN_1665311) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.365 MAPT NR NR 0.02 1.0202 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All MAPT (ILMN_2310814) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.512 MAPT NR NR -0.03 0.970446 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MAPT (ILMN_2310814) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.577 MAPT NR NR -0.01 0.99005 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All MAPT (ILMN_2310814) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.58 KIAA1267 NR NR -0.03 0.970446 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP KIAA1267 (ILMN_2200636) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.591 MAPT NR NR -0.06 0.941765 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MAPT (ILMN_2298727) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.615 MAPT NR NR -0.07 0.932394 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MAPT (ILMN_2298727) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.624 STH NR NR -0.02 0.980199 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD STH (ILMN_1665311) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.666 MAPT NR NR 0.01 1.01005 MAPT SNP-based eQTL 25324900 Caucasian MAYO 174 All MAPT (ILMN_2310814) expression in temporal cortex Expression intron_variant chr17 46003698 rs8070723 0.694 MAPT NR NR 0.01 1.01005 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAPT (ILMN_2310814) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 0.752 MAPT NR NR 0.04 1.04081 MAPT SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MAPT (ILMN_2310814) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 1.38E-08 MAPT NR NR -0.43 0.650509 MAPT SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MAPT (ILMN_1710903) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 1.49E-31 MAPT NR NR -0.43 0.650509 MAPT SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAPT (ILMN_1710903) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 1.50E-118 MAPT NA NA 5.11 5.11 MAPT SNP-based Disease Risk 22685416 Caucasian "Cohorts from Europe, USA" 8851 All Progressive Supranuclear Palsy (PSP) ADRD intron_variant chr17 46003698 rs8070723 2.10E-30 MAPT NR NR -0.44 0.644036 MAPT SNP-based eQTL 25324900 Caucasian MAYO 174 All MAPT(ILMN_1710903) expression in temporal cortex Expression intron_variant chr17 46003698 rs8070723 3.12E-37 MAPT NR NR -0.5 0.606531 MAPT SNP-based eQTL 22685416 Caucasian MAYO 202 AD MAPT (ILMN_1710903) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 7.02E-69 MAPT NR NR -0.47 0.625002 MAPT SNP-based eQTL 22685416 Caucasian MAYO 374 All MAPT (ILMN_1710903) expression in Cerebellar Expression intron_variant chr17 46003698 rs8070723 8.61E-44 MAPT NR NR -0.5 0.606531 MAPT SNP-based eQTL 22685416 Caucasian MAYO 399 All MAPT (ILMN_1710903) expression in Temporal cortex Expression intron_variant chr17 46003698 rs8070723 8.90E-31 MAPT NR NR -0.48 0.618783 MAPT SNP-based eQTL 25324900 Caucasian MAYO 181 All MAPT(ILMN_1710903) expression in Cerebellum Expression intron_variant chr17 46028029 rs7521 0.000011 MAPT NR NR 0.16 1.17351 MAPT SNP-based eQTL 25324900 Caucasian MAYO 182 All MAPT(ILMN_1710903) expression in Cerebellum Expression 3_prime_UTR_variant chr17 46028029 rs7521 0.00028 MAPT NR NR 0.12 1.1275 MAPT SNP-based eQTL 25324900 Caucasian MAYO 176 All MAPT(ILMN_1710903) expression in temporal cortex Expression 3_prime_UTR_variant chr17 46028029 rs7521 0.048 MAPT NR NR 0.08 1.08329 MAPT SNP-based eQTL 25324900 Caucasian MAYO 176 All MAPT (ILMN_2298727) expressionin temporal cortex Expression 3_prime_UTR_variant chr17 46028029 rs7521 0.084 MAPT NR NR 0.08 1.08329 MAPT SNP-based eQTL 25324900 Caucasian MAYO 182 All MAPT (ILMN_2298727) expressionin Cerebellum Expression 3_prime_UTR_variant chr17 46028029 rs7521 0.152 MAPT A A 1.08 1.08 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 5171 All LOAD Risk AD 3_prime_UTR_variant chr17 46028029 rs7521 0.437 MAPT A A 1.02 1.02 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 20827 All LOAD Risk AD 3_prime_UTR_variant chr17 46028029 rs7521 0.529 MAPT A A 1.02 1.02 MAPT SNP-based Disease risk 25324900 Caucasian ADGC 15656 All LOAD Risk AD 3_prime_UTR_variant chr17 46028029 rs7521 0.897 MAPT NR NR 0 1 MAPT SNP-based eQTL 25324900 Caucasian MAYO 176 All MAPT (ILMN_2310814) expression in temporal cortex Expression 3_prime_UTR_variant chr17 46028029 rs7521 0.976 MAPT NR NR 0 1 MAPT SNP-based eQTL 25324900 Caucasian MAYO 182 All MAPT (ILMN_2310814) expression in Cerebellum Expression 3_prime_UTR_variant chr17 46275856 rs2732703 0.00000064 "KANSL1, LRRC37A" G G 0.73 0.73 ARL17B SNP-based Disease risk 25778476 Caucasian IGAP 34152 APOE-e4- subjects AD AD intron_variant chr17 46275856 rs2732703 0.001 "KANSL1, LRRC37A" G G 0.71 0.71 ARL17B SNP-based Disease risk 25778476 Caucasian ADGC 2417 APOE-e4- subjects AD AD intron_variant chr17 46275856 rs2732703 5.80E-09 "KANSL1, LRRC37A" G G 0.73 0.73 ARL17B SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD intron_variant chr17 46278317 rs113986870 0.000000013 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44270189 - 44270252, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 0.00000016 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43716765 - 43716853, GRCh37) in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 0.0000026 MAPT NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "MAPT (44051752 - 44051833, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 0.000004 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43583231- 43583802, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 0.0000092 MAPT NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "MAPT (44051752 - 44051833, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 0.000013 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43723359 - 43723556, GRCh37) in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 0.00002 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43716765 - 43716853, GRCh37) in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 0.000024 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43583231- 43583802, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 0.000028 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44117069 - 44117161, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 0.000062 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44117069 - 44117161, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 0.000083 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43716765 - 43716853, GRCh37) in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 0.00064 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43583231- 43583802, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 0.00076 MAPT NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "MAPT (44051752 - 44051833, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 0.00098 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43723359 - 43723556, GRCh37) in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 0.004 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43723359 - 43723556, GRCh37) in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 0.008 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44117069 - 44117161, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 1.10E-13 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44249529 - 44249592, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 1.20E-11 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44249529 - 44249592, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 1.30E-09 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44270189 - 44270252, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 1.30E-11 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44270189 - 44270252, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 1.40E-15 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43583231- 43583802, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 1.40E-24 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44248224 - 44248977, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 1.60E-15 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44247654 - 44247852, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 1.70E-20 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43584264 - 43584884, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 2.50E-21 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44248224 - 44248977, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 2.60E-18 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44248224 - 44248977, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 3.00E-11 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44249529 - 44249592, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 3.00E-17 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44247654 - 44247852, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 3.30E-13 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43716765 - 43716853, GRCh37) in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 3.60E-09 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43584264 - 43584884, GRCh37) expression in temporal cortex (TCTX)" Expression intron_variant chr17 46278317 rs113986870 3.60E-14 MAPT NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "MAPT (44051752 - 44051833, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 4.00E-23 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44247654 - 44247852, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 4.30E-13 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44270189 - 44270252, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 4.90E-10 C17orf69 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "C17orf69 (43723359 - 43723556, GRCh37) in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 5.30E-10 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43584264 - 43584884, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 7.70E-16 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44249529 - 44249592, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46278317 rs113986870 7.80E-20 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44248224 - 44248977, GRCh37) expression in hippocampus (HIPP)" Expression intron_variant chr17 46278317 rs113986870 8.00E-11 LRRC37A4P NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "LRRC37A4P (43584264 - 43584884, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 8.00E-13 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44247654 - 44247852, GRCh37) expression in frontal cortex (FCTX)" Expression intron_variant chr17 46278317 rs113986870 9.80E-14 KANSL1 NR NR NR NA ARL17B SNP-based eQTL 25778476 Caucasian UKBEC 134 All "KANSL1 (44117069 - 44117161, GRCh37) expression in 10 brain regions (cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (specifically inferior olivary nucleus)(MEDU), occipital cortex (specifically primary visual cortex) (OCTX), putamen (PUTM), substantia nigra (SNIG), thalamus (THAL), temporal cortex (TCTX), intralobular white matter (WHMT))" Expression intron_variant chr17 46722680 rs7224296 0.000065 NSF NR NR NR NA NSF SNP-based Cross phenotype 29630712 Caucasian UKBEC NR All MAPT expression in brain Expression intron_variant chr17 46722680 rs7224296 0.00059 NSF NR NR NR NA NSF SNP-based Cross phenotype 29630712 Caucasian "ALS group, IGAP, FTGC, AFTD, PSP Genetics Consortium, IPDGC" 36052 All AD AD intron_variant chr17 46722680 rs7224296 3.30E-18 NSF NR NR NR NA NSF SNP-based Cross phenotype 29630712 Caucasian UKBEC NR All KIAA1267 expression in brain Expression intron_variant chr17 46722680 rs7224296 6.90E-11 NSF NR NR NR NA NSF SNP-based Cross phenotype 29630712 Caucasian UKBEC NR All MAPT (exon 3) expression in brain Expression intron_variant chr17 46765770 rs199528 0.000003 WNT3 C C NR NA WNT3 SNP-based eQTL 27899424 Caucasian UKBEC 101 All LRRC37A2 expression in Temporal cortex Expression intron_variant chr17 46765770 rs199528 0.00000959 WNT3 T T 0.85 0.85 WNT3 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr17 46765770 rs199528 0.00001 WNT3 C C NR NA WNT3 SNP-based eQTL 27899424 Caucasian UKBEC 101 All KANSL1 expression in Hippocampus Expression intron_variant chr17 46765770 rs199528 0.0000409 WNT3 NR NR NR NA WNT3 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr17 46765770 rs199528 0.0000409 WNT3 T T 0.82 0.82 WNT3 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intron_variant chr17 46765770 rs199528 0.03 WNT3 T T 0.89 0.89 WNT3 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intron_variant chr17 46770468 rs199525 0.0013 NR T T 0.36 1.43333 WNT3 SNP-based Endophenotype 27694991 African American "CHARGE, ENIGMA" 938 African Intracranial Volume Imaging intron_variant chr17 46770468 rs199525 0.406 NR T T 0.26 1.29693 WNT3 SNP-based Endophenotype 27694991 Asian "CHARGE, ENIGMA" 955 Asian Intracranial Volume Imaging intron_variant chr17 46770468 rs199525 0.407 NR T T 0.02 1.0202 WNT3 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 2363 European Intracranial Volume Imaging intron_variant chr17 46770468 rs199525 0.493 NR T T 0.04 1.04081 WNT3 SNP-based Endophenotype 27694991 Hispanic "CHARGE, ENIGMA" 1605 Hispanic Intracranial Volume Imaging intron_variant chr17 46770468 rs199525 3.80E-21 NR T T 0.1 1.10517 WNT3 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 26577 European Intracranial Volume Imaging intron_variant chr17 47297628 rs7221196 0.000000157 ITGB3 G G NR NA ITGB3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr17 47297628 rs7221196 0.000178 ITGB3 G G NR NA ITGB3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr17 47297628 rs7221196 0.37 ITGB3 G G 1 1 ITGB3 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr17 49219935 rs616338 0.0000216 ABI3 T T 1.42 1.42 ABI3 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 33786 All AD AD missense_variant chr17 49219935 rs616338 0.0000837 ABI3 T T 1.41 1.41 ABI3 SNP-based Disease risk 28714976 Caucasian "CHARGE, EADI, GERAD" 35831 All AD AD missense_variant chr17 49219935 rs616338 0.0175 ABI3 T T 1.58 1.58 ABI3 SNP-based Disease risk 28714976 Caucasian ADGC 14876 All AD AD missense_variant chr17 49219935 rs616338 4.56E-10 ABI3 T T 1.43 1.43 ABI3 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 84493 All AD AD missense_variant chr17 49255705 rs850520 0.000108 AK097513 A A NR NA PHOSPHO1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total triglycerides (TG) Non-ADRD intron_variant chr17 49255705 rs850520 0.000125 AK097513 A A NR NA PHOSPHO1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr17 49255705 rs850520 0.00024 AK097513 A A 1.01 1.01 PHOSPHO1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr17 49301409 rs2960171 0.0000872 ZNF652 C C NR NA ZNF652 SNP-based Cross phenotype 30413934 Caucasian CARDIoGRAMplusC4D 155197 All Coronary artery disease (CAD) Non-ADRD intron_variant chr17 49301409 rs2960171 0.000098 ZNF652 C C 1.01 1.01 ZNF652 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr17 49301409 rs2960171 0.000137 ZNF652 C C NR NA ZNF652 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr17 49373413 rs28394864 0.0000068 ABI3 A A NR NA ZNF652 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr17 49373413 rs28394864 0.0000729 ABI3 A A NR NA ZNF652 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr17 49373413 rs28394864 1.87E-08 ABI3 A A 5.62 NA ZNF652 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr17 49420891 rs8073041 2.17E-10 "PHB, LOC101927207" NR NR NR NA PHB SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker intron_variant chr17 49420891 rs8073041 7.87E-09 "PHB, LOC101927207" NR NR NR NA PHB SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker intron_variant chr17 49453879 rs79268972 2.55E-08 "PHB, LOC101927207" NR NR NR NA PHB SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker intron_variant chr17 49453879 rs79268972 8.17E-12 "PHB, LOC101927207" NR NR NR NA PHB SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker intron_variant chr17 49454994 rs77482998 4.61E-08 TNS3 (to be removed) NR NR NR NA PHB SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker intron_variant chr17 49454994 rs77482998 7.98E-12 TNS3 (to be removed) NR NR NR NA PHB SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker intron_variant chr17 58326988 rs2526378 0.000000273 BZRAP1 G G 0.94 0.94 TSPOAP1 SNP-based Disease risk 25862742 Caucasian "deCODE, DemGene, IGAP" 143878 All AD AD intron_variant chr17 58326988 rs2526378 0.000000834 BZRAP1 G G 0.94 0.94 TSPOAP1 SNP-based Disease risk 25862742 Caucasian IGAP 74046 All AD AD intron_variant chr17 58326988 rs2526378 0.00000122 BZRAPl NR NR NR NA TSPOAP1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr17 58326988 rs2526378 0.0000126 BZRAP1 NR NR 0.09 NA TSPOAP1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr17 58326988 rs2526378 0.00092 BZRAP1 G G 0.8 0.8 TSPOAP1 SNP-based Disease risk 25862742 Caucasian DemGene 2015 All AD AD intron_variant chr17 58326988 rs2526378 0.5 BZRAP1 G G 0.98 0.98 TSPOAP1 SNP-based Disease risk 25862742 Caucasian deCODE 67817 All AD AD intron_variant chr17 58331728 rs2632516 0.000000044 BZRAP1-AS1 C C 0.92 0.92 TSPOAP1 SNP-based Disease risk 28183528 Multi-ethnic "ADGC, IGAP" 59556 All AD AD intron_variant chr17 58331728 rs2632516 0.000000053 "MIR142, TSPOAP1-AS1" C C 0.94 0.94 TSPOAP1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD intron_variant chr17 58331728 rs2632516 0.00000023 "MIR142, TSPOAP1-AS1" C C 0.94 0.94 TSPOAP1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr17 58331728 rs2632516 0.00000056 BZRAP1-AS1 C C 0.91 0.91 TSPOAP1 SNP-based Disease risk 28183528 Multi-ethnic ADGC 33269 All AD AD intron_variant chr17 58331728 rs2632516 0.000000966 BZRAP1-AS1 C C -4.9 NA TSPOAP1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr17 58331728 rs2632516 0.005 BZRAP1-AS1 C C NR NA TSPOAP1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr17 58331728 rs2632516 0.01 BZRAP1-AS1 C C 0.94 0.94 TSPOAP1 SNP-based Disease risk 28183528 Caucasian IGAP 26287 All AD AD intron_variant chr17 58331728 rs2632516 0.075 "MIR142, TSPOAP1-AS1" C C 0.91 0.91 TSPOAP1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD intron_variant chr17 58331728 rs2632516 1.42E-09 BZRAP1-AS1 C C NR NA TSPOAP1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr17 61610481 rs2378873 2.03E-08 "BRIP1, NACA2" T T -0.53 0.588605 NACA2 SNP-based Endophenotype 29274321 Caucasian ADNI 206 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr17 63460787 rs138190086 0.0000075 ACE A A 1.29 1.29 CYB561 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD downstream_gene_variant chr17 63460787 rs138190086 0.00018 ACE A A 1.41 1.41 CYB561 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD downstream_gene_variant chr17 63460787 rs138190086 0.21 ACE A A 1.17 1.17 CYB561 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD downstream_gene_variant chr17 63460787 rs138190086 5.30E-09 ACE A A 1.3 1.3 CYB561 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD downstream_gene_variant chr17 63460787 rs138190086 7.50E-09 ACE A A 1.32 1.32 CYB561 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD downstream_gene_variant chr17 63468418 rs6504163 5.40E-09 NR T T 1.05 1.05 ACE SNP-based Disease risk 29777097 Caucasian UKBB 623001 All AD AD upstream_gene_variant chr17 63471115 rs4968782 0.000000046 ACE G G NR NA ACE SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF ACE Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 0.00000793 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma ACE Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 0.0000159 ACE G G NR NA ACE SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF ACE Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 0.000154 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF ACE Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 0.000406 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF ACE Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 0.0073 ACE NR NR -0.044 0.956954 ACE SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr17 63471115 rs4968782 0.72 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 0.83 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 1.61E-08 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF ACE Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 3.94E-12 ACE G G NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF ACE Fluid biomarker upstream_gene_variant chr17 63471115 rs4968782 8.39E-09 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.000000162 ACE C C NR NA ACE SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.000000225 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.0000097 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.000115 ACE C C NR NA ACE SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.000205 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.00117 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.0066 ACE NR NR -0.044 0.956954 ACE SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr17 63471587 rs4459609 0.37 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.55 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 0.79 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 1.09E-10 ACE C C NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF ACE Fluid biomarker upstream_gene_variant chr17 63471587 rs4459609 5.83E-08 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF ACE Fluid biomarker upstream_gene_variant chr17 63473168 rs1800764 0.03 ACE C C 0.85 0.85 ACE SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD upstream_gene_variant chr17 63484948 rs4316 0.000000011 ACE C C NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF ACE Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.0000096 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF ACE Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.0000198 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF ACE Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.000222 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF ACE Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.000397 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF ACE Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.0038 ACE NR NR -0.045 0.955997 ACE SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD synonymous_variant chr17 63484948 rs4316 0.0204 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma ACE Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.0247 ACE C C NR NA ACE SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF ACE Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.13 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.65 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker synonymous_variant chr17 63484948 rs4316 0.82 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker synonymous_variant chr17 63484948 rs4316 8.67E-09 ACE C C NR NA ACE SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.0000216 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.0000286 ACE NR NR -29.23 2.02103e-13 ACE SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.0000377 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.000051 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.000562 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.00126 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.0048 ACE NR NR -0.044 0.956954 ACE SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD synonymous_variant chr17 63488670 rs4343 0.02 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.0216 ACE G G NR NA ACE SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.71 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker synonymous_variant chr17 63488670 rs4343 0.85 ACE NR NR NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker synonymous_variant chr17 63488670 rs4343 3.71E-08 ACE G G NR NA ACE SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 5.20E-28 ACE NR NR -0.1 0.904837 ACE SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma ACE Fluid biomarker synonymous_variant chr17 63488670 rs4343 6.26E-08 ACE G G NR NA ACE SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF ACE Fluid biomarker synonymous_variant chr17 63492371 rs4351 0.047 ACE A A 1.42 1.42 ACE SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1321 All AD AD intron_variant chr17 63492371 rs4351 0.45 ACE A A 1.14 1.14 ACE SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1321 All Age of AD onset Other intron_variant chr17 66036434 rs1443291 0.00000224 NR NR NR 0.44 0.44 CEP112 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intron_variant chr17 66036434 rs1443291 0.0000258 CCDC46 NR NR 0.44 0.44 CEP112 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intron_variant chr17 66036434 rs1443291 0.0041 NR NR NR 0.61 0.61 CEP112 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intron_variant chr17 66036434 rs1443291 0.00636 CCDC46 NR NR 0.59 0.59 CEP112 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intron_variant chr17 66036434 rs1443291 0.0468 NR NR NR 0.58 0.58 CEP112 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intron_variant chr17 66036434 rs1443291 0.0571 NR NR NR 0.66 0.66 CEP112 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intron_variant chr17 66223079 rs8178841 0.00492 APOH NR NR -54.36 2.46463e-24 APOH SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma ApoH Fluid biomarker intron_variant chr17 66223079 rs8178841 1.08E-10 APOH NR NR -68.56 1.67792e-30 APOH SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma ApoH Fluid biomarker intron_variant chr17 66325449 rs8071250 0.000427 PRKCA C C 0.96 0.96 PRKCA SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr17 66325449 rs8071250 0.000596 PRKCA C C 0.96 0.96 PRKCA SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr17 66325449 rs8071250 0.000756 PRKCA C C NR NA PRKCA SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr17 66325449 rs8071250 0.00121 PRKCA C C NR NA PRKCA SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr17 66325449 rs8071250 0.0211 PRKCA C C 1 1 PRKCA SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr17 66325449 rs8071250 0.883 PRKCA C C 0.99 0.99 PRKCA SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr17 74979653 rs71380849 0.00000091 CDR2L A A 1.47 1.47 HID1 SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD downstream_gene_variant chr17 74979653 rs71380849 0.0000038 CDR2L A A 1.45 1.45 HID1 SNP-based Disease risk 25778476 Caucasian IGAP 34152 APOE-e4- subjects AD AD downstream_gene_variant chr17 74979653 rs71380849 0.04 CDR2L A A 1.59 1.59 HID1 SNP-based Disease risk 25778476 Caucasian ADGC 2417 APOE-e4- subjects AD AD downstream_gene_variant chr17 75875692 rs3744020 3.52E-11 NR A A 0.11 1.11628 TRIM47 SNP-based Endophenotype 29752348 Caucasian UKBB 8429 All White Matter Hyperintensity Volume Imaging intron_variant chr17 77948568 rs16970672 0.00000167 AC015804.1 NR NR 1.29 1.29 TNRC6C SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intergenic_region chr17 79053619 rs4790069 0.989 C1QTNF1 NR NR NR NA C1QTNF1 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology downstream_gene_variant chr18 1872316 rs1992269 0.000000977 NR A A 1.66 1.66 METTL4 SNP-based Disease risk 26049409 Asian Cohort from Japan 16983 All LOAD AD intergenic_region chr18 1872316 rs1992269 0.000216 NR A A 1.57 1.57 METTL4 SNP-based Disease risk 26049409 Asian Cohort from Japan 8208 All LOAD AD intergenic_region chr18 1872316 rs1992269 0.00096 NR A A 1.8 1.8 METTL4 SNP-based Disease risk 26049409 Asian Cohort from Japan 8775 All LOAD AD intergenic_region chr18 4133739 rs1402627 0.0000442 NR NR NR NR NA DLGAP1 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr18 5956471 rs3737355 0.0000107 L3MBTL4 NR NR NR NA L3MBTL4 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr18 6434982 rs76937036 0.000000046 NR A A 2.56 12.9358 L3MBTL4 SNP-based Endophenotype 25188341 Caucasian ADGC 2886 All Medial Temporal Sclerosis (MTS) Neuropathology downstream_gene_variant chr18 13890200 rs7230126 0.67 NR C C 0.03 1.03045 MC2R SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr18 23560468 rs1805081 0.157 NR G G 0.004 1.00401 NPC1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive missense_variant chr18 23560468 rs1805081 0.436 NR G G 1.02 1.02 NPC1 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD missense_variant chr18 23560468 rs1805081 0.832 NR G G 1.01 1.01 NPC1 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD missense_variant chr18 23560468 rs1805081 0.969 NR G G 1 1 NPC1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD missense_variant chr18 30214382 rs35242772 0.00000131 MIR302F C C 1.23 1.23 DSC3 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intergenic_region chr18 31488105 rs7239805 0.107 DSG2 A A 0.9 NA DSG3 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intergenic_region chr18 31508995 rs8093731 0.000000046 DSG2 T T 0.54 0.54 DSG2 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr18 31508995 rs8093731 0.0000111 DSG2 NR NR 0.706 2.02587 DSG2 SNP-based eQTL 30448613 Caucasian NABEC 85 All NETO1 (ILMN_1783168) expression in frontal cortex Expression intron_variant chr18 31508995 rs8093731 0.0001 DSG2 T T 0.73 0.73 DSG2 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr18 31508995 rs8093731 0.003 SUZ12P1 T T -2.17 NA DSG2 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr18 31508995 rs8093731 0.122 DSG2 T T 0.728 0.728 DSG2 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr18 31508995 rs8093731 0.766 SUZ12P1 T T NR NA DSG2 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr18 31508995 rs8093731 0.84 DSG2 T T 0.81 0.81 DSG2 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr18 31508995 rs8093731 0.9 DSG2 T T 1.01 1.01 DSG2 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr18 31508995 rs8093731 1.36E-08 DSG2 NR NR 0.77 2.15977 DSG2 SNP-based eQTL 30448613 Caucasian NABEC 85 All DLGAP1 (ILMN_2380779) expression in frontal cortex Expression intron_variant chr18 31508995 rs8093731 4.63E-08 SUZ12P1 T T NR NA DSG2 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr18 31508995 rs8093731 NR DSG2 C C 0.96 0.96 DSG2 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr18 31508995 rs8093731 NR ZCWPW1 C C 0.94 0.94 DSG2 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr18 32635093 rs1021599 0.000000881 NR T T NR NA KLHL14 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr18 45388569 rs73431975 0.0000017 SLC14A2 NR NR 0.573 1.77358 SLC14A2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr18 45388569 rs73431975 0.000082 SLC14A2 NR NR 0.584 1.7932 SLC14A2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr18 45388569 rs73431975 0.0191 SLC14A2 NR NR 0.489 1.63068 SLC14A2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr18 47160932 rs2635049 0.0000912 NR NR NR 1.95 1.95 AC012254.2 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intron_variant chr18 47160932 rs2635049 0.000195 NR NR NR 1.89 1.89 AC012254.2 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intron_variant chr18 47160932 rs2635049 0.00268 NR NR NR 1.92 1.92 AC012254.2 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intron_variant chr18 47160932 rs2635049 0.0188 NR NR NR 1.92 1.92 AC012254.2 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intron_variant chr18 49495404 rs17656050 0.00938 RPL17 G G NR NA RPL17 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD non_coding_transcript_exon_variant chr18 49495404 rs17656050 3.87E-113 NR G G NR NA RPL17 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group RPL17 (ILMN_1655422) expression Expression non_coding_transcript_exon_variant chr18 49605411 rs9954848 0.000458 LIPG A A NR NA LIPG SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr18 49605411 rs9954848 0.00109 LIPG A A NR NA LIPG SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intergenic_region chr18 49605411 rs9954848 0.00112 LIPG A A 0.96 0.96 LIPG SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr18 49605411 rs9954848 0.00161 LIPG A A 0.96 0.96 LIPG SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr18 49605411 rs9954848 0.123 LIPG A A 1 1 LIPG SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr18 49605411 rs9954848 0.422 LIPG A A 0.96 0.96 LIPG SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr18 52244453 rs1445093 0.000000775 NR C C NR NA DCC SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF T-tau Fluid biomarker intergenic_region chr18 55487771 rs9960767 0.027 TCF4 NR NR 0.67 0.67 TCF4 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr18 55487771 rs9960767 0.5 TCF4 NR NR 0.93 0.93 TCF4 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr18 58522227 rs76726049 0.000000033 ALPK2 C C 5.52 NA ALPK2 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr18 58522227 rs76726049 0.000000183 ALPK2 C C NR NA ALPK2 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr18 58522227 rs76726049 0.039 ALPK2 C C NR NA ALPK2 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr18 58875863 rs12964543 0.000112 ZNF532 A A 1.24 1.24 ZNF532 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intron_variant chr18 58875863 rs12964543 0.000112 ZNF532 NR NR NR NA ZNF532 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr18 58875863 rs12964543 0.00091 ZNF532 A A 1.12 1.12 ZNF532 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr18 58875863 rs12964543 0.24 ZNF532 A A 1.05 1.05 ZNF532 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intron_variant chr18 59084822 rs1037757 0.00000829 "LOC390958, Sec11C" NR NR NR NA SEC11C SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other non_coding_transcript_exon_variant chr18 59084822 rs1037757 0.0000136 "LOC390958, Sec11C" NR NR NR NA SEC11C SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other non_coding_transcript_exon_variant chr18 59084822 rs1037757 0.0000293 "LOC390958, Sec11C" NR NR -4.56 0.0104621 SEC11C SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other non_coding_transcript_exon_variant chr18 59084822 rs1037757 0.0369 "LOC390958, Sec11C" NR NR -2.26 0.10435 SEC11C SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other non_coding_transcript_exon_variant chr18 59084822 rs1037757 0.71 "LOC390958, Sec11C" NR NR -3.45 0.0317456 SEC11C SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other non_coding_transcript_exon_variant chr18 60172536 rs571312 0.27 NR A A 1.051 1.051 MC4R SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr18 60172536 rs571312 0.316 NR A A 0.975 0.975 MC4R SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr18 60172536 rs571312 0.47 NR A A 0.961 0.961 MC4R SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr18 60172536 rs571312 0.924 NR A A 0 1 MC4R SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr18 61948797 rs72934313 0.655 RNF152 C C 1.07 1.07 PIGN SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr18 62566413 rs11152349 0.0000324 ZCCHC2 NR NR NR NA ZCCHC2 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr18 64058306 rs11152416 0.0000935 NR NR NR 2.12 2.12 SERPINB8 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr18 64058306 rs11152416 0.0154 NR NR NR 1.62 1.62 SERPINB8 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr18 64058306 rs11152416 0.0769 NR NR NR 1.49 1.49 SERPINB8 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr18 64058306 rs11152416 0.107 NR NR NR 1.55 1.55 SERPINB8 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr18 73391387 rs1943816 0.000000108 NR C C NR NA NETO1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF P-tau181p Fluid biomarker intergenic_region chr18 73391387 rs1943816 0.00000015 NR C C NR NA NETO1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF P-tau181p Fluid biomarker intergenic_region chr18 76997395 rs3794851 0.0000034 NR C C 1.05 2.85765 MBP SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr18 76997395 rs3794851 0.0067 NR C C 0.36 1.43333 MBP SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr18 76997395 rs3794851 0.93 NR C C -0.01 0.99005 MBP SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr18 78743253 rs9945493 0.000000171 NR NR NR NR NA SALL3 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr18 78743253 rs9945493 0.000005 NR NR NR 0.33 0.33 SALL3 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr18 78743253 rs9945493 0.00000897 NR NR NR NR NA SALL3 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr18 78743253 rs9945493 0.000263 NR NR NR 0.23 0.23 SALL3 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr18 78743253 rs9945493 0.000494 NR NR NR NR NA SALL3 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr18 78743253 rs9945493 0.0104 NR NR NR 0.38 0.38 SALL3 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr18 78743253 rs9945493 0.914 NR NR NR NR NA SALL3 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intergenic_region chr18 78743253 rs9945493 0.94111 NR NR NR NR NA SALL3 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr18 78743253 rs9945493 NA NR NR NR NR NA SALL3 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr18 79621649 rs12961169 0.0000116 GLIS1 NR NR 0.05 1.05127 CTDP1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF P-tau181p Fluid biomarker intergenic_region chr18 79621649 rs12961169 0.0000137 GLIS1 T T 0.04 1.04081 CTDP1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF T-tau Fluid biomarker intergenic_region chr18 79621649 rs12961169 0.0000358 GLIS1 NR NR 0.05 1.05127 CTDP1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF P-tau181p Fluid biomarker intergenic_region chr18 79621649 rs12961169 0.0113 GLIS1 T T 0.016 1.01613 CTDP1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF Ab1-42 Fluid biomarker intergenic_region chr18 79621649 rs12961169 0.0934 GLIS1 T T 0.12 1.1275 CTDP1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1530 All AD Progression (based on CDR Score) Cognitive intergenic_region chr18 79621649 rs12961169 0.193 GLIS1 T T 1.03 2.80107 CTDP1 SNP-based Disease risk 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 74046 All AD risk AD intergenic_region chr18 79621649 rs12961169 0.249 GLIS1 T T 0.04 1.04081 CTDP1 SNP-based Age at onset (AAO) / Survival 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 39855 AD subjects Age at onset Other intergenic_region chr18 79621649 rs12961169 5.12E-10 GLIS1 NR NR 0.05 1.05127 CTDP1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF P-tau181p Fluid biomarker intergenic_region chr18 79621649 rs12961169 5.12E-10 GLIS1 T T 0.05 1.05127 CTDP1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF P-tau181p Fluid biomarker intergenic_region chr19 1001778 rs115882880 6.34E-08 GRIN3B A A 1.55 1.55 GRIN3B SNP-based Disease risk 23571587 African American ADGC 5896 All LOAD AD intron_variant chr19 1021628 rs117481827 0.00316 C19orf6 NR NR -0.09 NA TMEM259 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other upstream_gene_variant chr19 1031213 rs7247087 0.000000103 ABCA7 A A 0.18 1.19722 CNN2 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data ABCA7 (ILMN_1743205) expression in Cerebellar tissue (CER) Expression intron_variant chr19 1031213 rs7247087 0.0000353 ABCA7 A A 0.14 1.15027 CNN2 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data ABCA7 (ILMN_1743205) expression in Temporal cortex (TCX) Expression intron_variant chr19 1031213 rs7247087 NS ABCA7 A A 1.03 2.80107 CNN2 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD intron_variant chr19 1039324 rs111278892 7.93E-11 INPPD5 G G 6.5 NA CNN2 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD upstream_gene_variant chr19 1044713 rs3764647 0.0087 ABCA7 G G 1.32 1.32 ABCA7 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD missense_variant chr19 1046521 rs3764650 0.00000025 ABCA7 NR NR NR NA ABCA7 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 1046521 rs3764650 0.00000026 ABCA7 NR NR 1.22 1.22 ABCA7 SNP-based Disease risk 21460840 Caucasian "ADC, EADI, GERAD" 20373 All AD AD intron_variant chr19 1046521 rs3764650 0.00000029 ABCA7 NR NR 1.22 1.22 ABCA7 SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI" 29544 All AD AD intron_variant chr19 1046521 rs3764650 0.000019 ABCA7 NR NR 1.28 1.28 ABCA7 SNP-based Disease risk 21460840 Caucasian GERAD 9799 All AD AD intron_variant chr19 1046521 rs3764650 0.019 ABCA7 G G 1.27 1.27 ABCA7 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 1046521 rs3764650 0.02 ABCA7 NR NR 1.39 1.39 ABCA7 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr19 1046521 rs3764650 0.03 NR G G 0.18 1.19722 ABCA7 SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology intron_variant chr19 1046521 rs3764650 0.0366 ABCA7 G G 1.13 1.13 ABCA7 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr19 1046521 rs3764650 4.50E-17 ABCA7 NR NR 1.23 1.23 ABCA7 SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI, GERAD" 59716 All AD AD intron_variant chr19 1046521 rs3764650 5.00E-21 ABCA7 NR NR 1.23 1.23 ABCA7 SNP-based Disease risk 21460840 Caucasian "ADGC, GERAD" NR All AD AD intron_variant chr19 1050131 rs7408475 0.0000501 ABCA7 NR NR 0.18 NA ABCA7 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr19 1050421 rs115550680 2.21E-09 ABCA7 G G 1.79 1.79 ABCA7 SNP-based Disease risk 23571587 African American ADGC 5896 All LOAD AD intron_variant chr19 1053525 rs3752241 2.87E-08 ABCA7 G G NR NA ABCA7 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD synonymous_variant chr19 1056493 rs3752246 0.000000047 ABCA7 G G 1.18 1.18 ABCA7 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD missense_variant chr19 1056493 rs3752246 0.000000497 ABCA7 G G 1.15 1.15 ABCA7 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD missense_variant chr19 1056493 rs3752246 0.000000579 ABCA7 G G 1.15 1.15 ABCA7 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD missense_variant chr19 1056493 rs3752246 0.0000102 ABCA7 G G 1.16 1.16 ABCA7 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD missense_variant chr19 1056493 rs3752246 0.0000193 ABCA7 G G 1.15 1.15 ABCA7 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD missense_variant chr19 1056493 rs3752246 0.0027 ABCA7 NR NR 1.11 1.11 ABCA7 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD missense_variant chr19 1056493 rs3752246 0.00907 ABCA7 G G 1.13 1.13 ABCA7 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD missense_variant chr19 1056493 rs3752246 0.0123 ABCA7 G G 1.13 1.13 ABCA7 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD missense_variant chr19 1056493 rs3752246 0.242 ABCA7 G G -0.19 0.826959 ABCA7 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other missense_variant chr19 1056493 rs3752246 0.375 ABCA7 G G 0.82 0.82 ABCA7 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD missense_variant chr19 1056493 rs3752246 0.7 ABCA7 G G -0.27 0.763379 ABCA7 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other missense_variant chr19 1056493 rs3752246 3.10E-16 ABCA7 G G 1.15 1.15 ABCA7 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD missense_variant chr19 1056493 rs3752246 3.98E-09 ABCA7 NR NR -0.25 NA ABCA7 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other missense_variant chr19 1056493 rs3752246 6.60E-10 ABCA7 G G 1.13 1.13 ABCA7 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD missense_variant chr19 1063444 rs4147929 0.000000099 ABCA7 A A 1.17 1.17 ABCA7 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr19 1063444 rs4147929 0.00000394 ABCA7 NR NR 0.259 1.29563 ABCA7 SNP-based eQTL 30448613 Caucasian UKBEC 49 All EID2B (t3862068) expression in frontal cortex Expression intron_variant chr19 1063444 rs4147929 0.0011 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in intra-locular white matter (WHMT) Expression intron_variant chr19 1063444 rs4147929 0.00139 ABCA7 NR NR 1.12 1.12 ABCA7 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD intron_variant chr19 1063444 rs4147929 0.0018 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in thalamus (THAL) Expression intron_variant chr19 1063444 rs4147929 0.0037 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in temporal cortex (TCTX) Expression intron_variant chr19 1063444 rs4147929 0.005 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in substantia nigra (SNIG) Expression intron_variant chr19 1063444 rs4147929 0.0088 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in putamen (PUTM) Expression intron_variant chr19 1063444 rs4147929 0.01 ABCA7 A A 1.32 1.32 ABCA7 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr19 1063444 rs4147929 0.014 ABCA7 A A 1.24 1.24 ABCA7 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr19 1063444 rs4147929 0.02 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in hippocampus (HIPP) Expression intron_variant chr19 1063444 rs4147929 0.05 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in temporal cortex (TCTX) Expression intron_variant chr19 1063444 rs4147929 0.06 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in frontal cortex (FCTX) Expression intron_variant chr19 1063444 rs4147929 0.06 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in putamen (PUTM) Expression intron_variant chr19 1063444 rs4147929 0.18 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in intra-locular white matter (WHMT) Expression intron_variant chr19 1063444 rs4147929 0.2 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in occipital cortex (OCTX) Expression intron_variant chr19 1063444 rs4147929 0.22 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in intra-locular white matter (WHMT) Expression intron_variant chr19 1063444 rs4147929 0.23 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in medulla (MEDU) Expression intron_variant chr19 1063444 rs4147929 0.26 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in temporal cortex (TCTX) Expression intron_variant chr19 1063444 rs4147929 0.3 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in substantia nigra (SNIG) Expression intron_variant chr19 1063444 rs4147929 0.3 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in hippocampus (HIPP) Expression intron_variant chr19 1063444 rs4147929 0.32 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in thalamus (THAL) Expression intron_variant chr19 1063444 rs4147929 0.42 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in occipital cortex (OCTX) Expression intron_variant chr19 1063444 rs4147929 0.44 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in cerebellar cortex (CRBL) Expression intron_variant chr19 1063444 rs4147929 0.52 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in medulla (MEDU) Expression intron_variant chr19 1063444 rs4147929 0.52 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in occipital cortex (OCTX) Expression intron_variant chr19 1063444 rs4147929 0.57 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in substantia nigra (SNIG) Expression intron_variant chr19 1063444 rs4147929 0.61 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in frontal cortex (FCTX) Expression intron_variant chr19 1063444 rs4147929 0.65 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in putamen (PUTM) Expression intron_variant chr19 1063444 rs4147929 0.67 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in medulla (MEDU) Expression intron_variant chr19 1063444 rs4147929 0.68 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in intra-locular white matter (WHMT) Expression intron_variant chr19 1063444 rs4147929 0.7 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in putamen (PUTM) Expression intron_variant chr19 1063444 rs4147929 0.71 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in hippocampus (HIPP) Expression intron_variant chr19 1063444 rs4147929 0.71 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in substantia nigra (SNIG) Expression intron_variant chr19 1063444 rs4147929 0.74 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in frontal cortex (FCTX) Expression intron_variant chr19 1063444 rs4147929 0.76 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in thalamus (THAL) Expression intron_variant chr19 1063444 rs4147929 0.79 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in cerebellar cortex (CRBL) Expression intron_variant chr19 1063444 rs4147929 0.8 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in temporal cortex (TCTX) Expression intron_variant chr19 1063444 rs4147929 0.89 SBNO2 NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects SBNO2 (t3844978) expression in cerebellar cortex (CRBL) Expression intron_variant chr19 1063444 rs4147929 0.91 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in frontal cortex (FCTX) Expression intron_variant chr19 1063444 rs4147929 0.91 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in hippocampus (HIPP) Expression intron_variant chr19 1063444 rs4147929 0.91 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844969) expression in thalamus (THAL) Expression intron_variant chr19 1063444 rs4147929 0.91 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (t3844952) expression in cerebellar cortex (CRBL) Expression intron_variant chr19 1063444 rs4147929 0.93 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in occipital cortex (OCTX) Expression intron_variant chr19 1063444 rs4147929 1 POLR2E NR NR NR NA ABCA7 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects POLR2E (3844957) expression in medulla (MEDU) Expression intron_variant chr19 1063444 rs4147929 1.10E-15 ABCA7 A A 1.15 1.15 ABCA7 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr19 1063444 rs4147929 1.70E-09 ABCA7 A A 1.14 1.14 ABCA7 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr19 1063444 rs4147929 8.64E-09 ABCA7 G G NR NA ABCA7 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr19 1063444 rs4147929 NR ABCA7 A A 1.66 1.66 ABCA7 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr19 1063444 rs4147929 NR ZCWPW1 A A 1.25 1.25 ABCA7 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr19 1063444 rs4147929 NR ZCWPW1 A A 1.81 1.81 ABCA7 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr19 1065946 rs2242436 0.0441 ABCA7 A A 0.84 NA ARHGAP45 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other 5_prime_UTR_premature_start_codon_gain_variant chr19 1073074 rs2072102 0.00000357 ABCA7 A A 0.15 1.16183 ARHGAP45 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data ABCA7 (ILMN_1743205) expression in Cerebellar tissue (CER) Expression intron_variant chr19 1073074 rs2072102 0.0000674 ABCA7 A A 1.11 3.03436 ARHGAP45 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD intron_variant chr19 1073074 rs2072102 0.00112 ABCA7 A A 0.11 1.11628 ARHGAP45 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data ABCA7 (ILMN_1743205) expression in Temporal cortex (TCX) Expression intron_variant chr19 1075980 rs757232 0.00000262 ABCA7 A A 0.15 1.16183 ARHGAP45 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data ABCA7 (ILMN_1743205) expression in Cerebellar tissue (CER) Expression intron_variant chr19 1075980 rs757232 0.0000625 ABCA7 A A 1.11 3.03436 ARHGAP45 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD intron_variant chr19 1075980 rs757232 0.00161 ABCA7 A A 0.1 1.10517 ARHGAP45 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data ABCA7 (ILMN_1743205) expression in Temporal cortex (TCX) Expression intron_variant chr19 1082845 rs115553053 3.14E-08 HMHA1 T T 1.86 1.86 ARHGAP45 SNP-based Disease risk 23571587 African American ADGC 5896 All LOAD AD synonymous_variant chr19 1207239 rs3764640 0.00000788 STK11 NR NR 0.68 0.68 STK11 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr19 1400867 rs3786974 0.0264 GAMT T T NR NA GAMT SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr19 1400867 rs3786974 1.35E-18 NR T T NR NA GAMT SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group GAMT (ILMN_1756469) expression Expression intron_variant chr19 1400867 rs3786974 5.93E-09 NR T T NR NA GAMT SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group GAMT (ILMN_1794595) expression Expression intron_variant chr19 3405594 rs9749589 0.0025 NR NR NR 1.17 1.17 NFIC SNP-based Disease risk 28183528 Multi-ethnic ADGC 33269 All AD AD intron_variant chr19 3405594 rs9749589 0.0033 NR NR NR 1.1 1.1 NFIC SNP-based Disease risk 28183528 Multi-ethnic "ADGC, IGAP" 59556 All AD AD intron_variant chr19 3405594 rs9749589 0.5 NR NR NR 1.04 1.04 NFIC SNP-based Disease risk 28183528 Caucasian IGAP 26287 All AD AD intron_variant chr19 3647903 rs12984273 0.00271 CACTIN T T NR NA PIP5K1C SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr19 3647903 rs12984273 1.30E-21 NR T T NR NA PIP5K1C SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group CACTIN (ENSG00000105298) expression Expression intron_variant chr19 6614651 rs61111347 0.63 NR A A -0.08 0.923116 CD70 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intergenic_region chr19 6636828 rs149933701 0.0000016 NR C C 10.68 43477.6 TNFSF14 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intergenic_region chr19 6636828 rs149933701 0.008 NR C C 0.36 1.43333 TNFSF14 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intergenic_region chr19 10284116 rs1799969 0.00000103 ICAM1 NR NR -0.08 0.923116 ICAM1 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma ICAM-1 Fluid biomarker missense_variant chr19 17631660 rs4239633 0.00000198 UNC13A NR NR NR NA UNC13A SNP-based Cross phenotype 29630712 Caucasian "ALS group, IGAP, FTGC, AFTD, PSP Genetics Consortium, IPDGC" 36052 All AD AD intron_variant chr19 17631660 rs4239633 0.001 UNC13A NR NR NR NA UNC13A SNP-based Cross phenotype 29630712 Caucasian UKBEC NR All ELL expression in brain Expression intron_variant chr19 18422832 rs7258465 0.0000326 SSBP4 T T NR NA SSBP4 SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD intron_variant chr19 18422832 rs7258465 0.000126 "DKFZp586K0821, NDUFS3" T T NR NA SSBP4 SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 16559 All Type 1 diabetes (T1D) Non-ADRD intron_variant chr19 19250926 rs1064395 0.25 NCAN NR NR 1.08 1.08 NCAN SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD 3_prime_UTR_variant chr19 19250926 rs1064395 0.29 NCAN NR NR 1.1 1.1 NCAN SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD 3_prime_UTR_variant chr19 29245435 rs11083866 0.00000538 LOC400794 NR NR 114.77 69819653317255026275047162222818561392730781515776 UQCRFS1 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intergenic_region chr19 29245435 rs11083866 0.00074 LOC400794 A A 114.32 44518976491554210011864262016132115227552656654336 UQCRFS1 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr19 29245435 rs11083866 0.0016 LOC400794 A A NR NA UQCRFS1 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr19 29245435 rs11083866 0.0023 LOC400794 A A 115.32 121015124818587235646718167356365894143602696650752 UQCRFS1 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intergenic_region chr19 33161450 rs11084710 0.000045 WDR88 NR NR 2.43 2.43 WDR88 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr19 33818627 rs29941 0.155 NR G G 0.968 0.968 KCTD15 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD downstream_gene_variant chr19 33818627 rs29941 0.65 NR G G 0.983 0.983 KCTD15 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD downstream_gene_variant chr19 33818627 rs29941 0.731 NR G G 0.98 0.98 KCTD15 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD downstream_gene_variant chr19 33818627 rs29941 0.907 NR G G 0 1 KCTD15 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive downstream_gene_variant chr19 34165501 rs587259 0.0002 LSM14A T T NR NA LSM14A SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr19 34165501 rs587259 0.00028 LSM14A T T NR NA LSM14A SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr19 34165501 rs587259 0.0009 LSM14A T T NR NA LSM14A SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr19 35534023 rs4806173 0.509 GAPDHS G G 0.95 0.95 GAPDHS SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr19 35658859 rs4806187 1.02E-35 UPK1A NR NR -0.72 0.486752 COX6B1 SNP-based eQTL 22685416 Caucasian MAYO 399 All UPK1A expression in Temporal cortex Expression splice_region_variant chr19 35658859 rs4806187 1.25E-59 UPK1A NR NR -1.04 0.353455 COX6B1 SNP-based eQTL 22685416 Caucasian MAYO 374 All UPK1A expression in Cerebellar Expression splice_region_variant chr19 35658859 rs4806187 2.55E-32 UPK1A NR NR -1.05 0.349938 COX6B1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD UPK1A expression in Cerebellar Expression splice_region_variant chr19 35658859 rs4806187 3.05E-21 UPK1A NR NR -0.99 0.371577 COX6B1 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD UPK1A expression in Cerebellar Expression splice_region_variant chr19 43988990 rs393195 0.0002 ZNF155 G G NR NA ZNF155 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 43988990 rs393195 0.00071 ZNF155 G G NR NA ZNF155 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr19 43988990 rs393195 0.0147 ZNF155 G G NR NA ZNF155 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 44095462 rs4459653 0.000008 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr19 44096224 rs4802207 0.00000923 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD 5_prime_UTR_variant chr19 44107267 rs4508518 0.00000195 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD missense_variant chr19 44107267 rs4508518 0.0000437 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD missense_variant chr19 44107267 rs4508518 0.0263 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD missense_variant chr19 44108078 rs3746319 0.00000301 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD missense_variant chr19 44108078 rs3746319 0.0000296 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD missense_variant chr19 44108078 rs3746319 0.0000605 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD missense_variant chr19 44108078 rs3746319 0.0233 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD missense_variant chr19 44109508 rs2061332 0.00000491 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr19 44109508 rs2061332 0.0000393 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr19 44109508 rs2061332 0.0000619 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr19 44109508 rs2061332 0.0379 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr19 44110055 rs2061333 0.00000151 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr19 44110055 rs2061333 0.0000251 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr19 44110055 rs2061333 0.0175 ZNF224 NR NR NR NA ZNF224 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr19 44129800 rs10406335 0.0003 ZNF225 G G NR NA ZNF225 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 44129800 rs10406335 0.0009 ZNF225 G G NR NA ZNF225 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 44129800 rs10406335 0.0039 ZNF225 G G NR NA ZNF225 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr19 44547413 rs17714718 1.48E-08 CEACAM22P NR NR NR NA CEACAM20 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD non_coding_transcript_exon_variant chr19 44570931 rs846848 0.00000252 "CEACAM22P, LOC147710" NR NR NR NA CEACAM20 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44642803 rs7255066 5.27E-10 PVR NR NR NR NA PVR SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44662645 rs714948 2.03E-10 PVR A A 1.6 1.6 PVR SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD 3_prime_UTR_variant chr19 44662645 rs714948 6.26E-13 PVR NR NR NR NA PVR SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr19 44698757 rs12150984 2.12E-09 CEACAM16 NR NR NR NA CEACAM16 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44722081 rs2965109 0.0027 "BCL3, CEACAM16" T T 0.92 0.92 CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44722081 rs2965109 0.0027 CEACAM16/BCL3 T T NR NA CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44722081 rs2965109 0.04 CEACAM16/BCL3 T T NR NA CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44722081 rs2965109 0.042 "BCL3, CEACAM16" T T 0.94 0.94 CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44724478 rs7254776 0.0036 "BCL3, CEACAM16" T T 1.08 1.08 CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD downstream_gene_variant chr19 44724478 rs7254776 0.0036 CEACAM16/BCL3 T T NR NA CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD downstream_gene_variant chr19 44724478 rs7254776 0.12 "BCL3, CEACAM16" T T 1.04 1.04 CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD downstream_gene_variant chr19 44724478 rs7254776 0.12 CEACAM16/BCL3 T T NR NA CEACAM16 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD downstream_gene_variant chr19 44728212 rs2927488 0.00000286 NR A A NR NA CEACAM16 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD upstream_gene_variant chr19 44734556 rs2965101 0.00000209 NR C C NR NA BCL3 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intergenic_region chr19 44734556 rs2965101 0.0055 "BCL3, CEACAM16" T T 1.07 1.07 BCL3 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intergenic_region chr19 44734556 rs2965101 0.0055 CEACAM16/BCL3 T T NR NA BCL3 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intergenic_region chr19 44734556 rs2965101 0.2 "BCL3, CEACAM16" T T 1.03 1.03 BCL3 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intergenic_region chr19 44734556 rs2965101 0.2 CEACAM16/BCL3 T T NR NA BCL3 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intergenic_region chr19 44738850 rs2927438 0.000000332 NR A A 1.35 1.35 BCL3 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intergenic_region chr19 44738850 rs2927438 5.69E-29 BCL3 NR NR NR NA BCL3 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr19 44738916 rs1531517 5.83E-12 "CEACAM16, BCL3" NR NR NR NA BCL3 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr19 44744370 rs4803750 0.008 BCL3 NR NR -0.02 0.980199 BCL3 SNP-based Endophenotype 30805717 Caucasian MAGIC 51750 All Fasting Insulin Fluid biomarker upstream_gene_variant chr19 44744370 rs4803750 9.04E-13 BCL3 NR NR -0.24 0.786628 BCL3 SNP-based Endophenotype 30805717 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr19 44749847 rs8100239 1.50E-22 BCL3 NR NR NR NA BCL3 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44750911 rs8103315 1.87E-08 BCL3 A A 1.5 1.5 BCL3 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44810458 rs2927477 4.04E-11 BCAM NR NR NR NA BCAM SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44823407 rs10405693 2.83E-12 BCAM T T 1.49 1.49 BCAM SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD downstream_gene_variant chr19 44825957 rs10402271 0.000000147 NR G G NR NA BCAM SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD downstream_gene_variant chr19 44825957 rs10402271 0.000000214 NR C C 1.26 1.26 BCAM SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD downstream_gene_variant chr19 44825957 rs10402271 0.000000726 NR C C 1.39 1.39 BCAM SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD downstream_gene_variant chr19 44825957 rs10402271 0.000277 NR C C 1.23 1.23 BCAM SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD downstream_gene_variant chr19 44825957 rs10402271 1.98E-17 BCAM G G 1.46 1.46 BCAM SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD downstream_gene_variant chr19 44848259 rs41289512 2.70E-194 APOE G G NR NA NECTIN2 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr19 44848259 rs41289512 5.79E-276 APOE G G 35.5 NA NECTIN2 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr19 44848489 rs1871047 0.000000487 PVRL2 G G 0.79 0.79 NECTIN2 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44848489 rs1871047 2.20E-18 PVRL2 NR NR NR NA NECTIN2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44857967 rs440277 0.000000479 PVRL2 A A 0.76 0.76 NECTIN2 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44859410 rs377702 0.000000199 PVRL2 A A 1.29 1.29 NECTIN2 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44875803 rs387976 4.39E-12 PVRL2 NR NR NR NA NECTIN2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44876534 rs11667640 1.12E-09 PVRL2 NR NR NR NA NECTIN2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44878777 rs6859 0.000000096 PVRL2 A A 1.41 1.41 NECTIN2 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 0.000000106 PVRL2 A A 1.41 1.41 NECTIN2 SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 0.000000539 PVRL2 A A 1.58 1.58 NECTIN2 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 0.0000006 PVRL2 A A NR NA NECTIN2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 0.00000613 PVRL2 A A 1.7 1.7 NECTIN2 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 0.0000287 PVRL2 A A 1.4 NA NECTIN2 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic CHARGE 5018 All Age at onset Other 3_prime_UTR_variant chr19 44878777 rs6859 0.0000534 PVRL2 A A 1.4 1.4 NECTIN2 SNP-based Disease risk 29107063 Multi-ethnic CHARGE 5018 All AD AD 3_prime_UTR_variant chr19 44878777 rs6859 0.0087 PVRL2 A A 1.3 1.3 NECTIN2 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 0.042 PVRL2 NR NR NR NA NECTIN2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD 3_prime_UTR_variant chr19 44878777 rs6859 1.12E-18 PVRL2 A A 1.7 1.7 NECTIN2 SNP-based Disease risk 29107063 Multi-ethnic ADGC 4561 All AD AD 3_prime_UTR_variant chr19 44878777 rs6859 1.48E-10 NR A A NR NA NECTIN2 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD 3_prime_UTR_variant chr19 44878777 rs6859 1.73E-10 PVRL2 A A NR NA NECTIN2 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 3.31E-96 PVRL2 NR NR NR NA NECTIN2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr19 44878777 rs6859 6.09E-14 PVRL2 A A NR NA NECTIN2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD 3_prime_UTR_variant chr19 44878777 rs6859 6.90E-41 APOE NR NR 1.46 1.46 NECTIN2 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD 3_prime_UTR_variant chr19 44878777 rs6859 7.87E-28 PVRL2 A A 1.7 1.7 NECTIN2 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD 3_prime_UTR_variant chr19 44879804 rs3852861 0.0000599 TOMM40 T T 0.64 0.64 NECTIN2 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44879804 rs3852861 0.038 TOMM40 T T 0.78 0.78 NECTIN2 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44879804 rs3852861 5.32E-11 PVRL2 T T 0.64 0.64 NECTIN2 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44882502 rs3745150 0.0036 PVRL2 C C 1.11 1.11 NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44882502 rs3745150 0.005 PVRL2 C C NR NA NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44882502 rs3745150 0.42 PVRL2 C C 1.03 1.03 NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44882502 rs3745150 0.42 PVRL2 C C NR NA NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44884202 rs12972156 0.00000153 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884202 rs12972156 0.00000495 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr19 44884202 rs12972156 0.0000672 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884202 rs12972156 0.00837 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884202 rs12972156 0.00926 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884202 rs12972156 1.10E-09 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884202 rs12972156 1.21E-10 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884202 rs12972156 2.31E-15 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884202 rs12972156 3.03E-15 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884202 rs12972156 6.35E-37 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44884339 rs12972970 0.00000104 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884339 rs12972970 0.00000324 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr19 44884339 rs12972970 0.0000996 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884339 rs12972970 0.00974 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884339 rs12972970 0.0125 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884339 rs12972970 1.28E-15 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884339 rs12972970 3.74E-40 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44884339 rs12972970 5.94E-10 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884339 rs12972970 7.83E-11 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884339 rs12972970 8.24E-16 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884873 rs34342646 0.00000104 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884873 rs34342646 0.00000302 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr19 44884873 rs34342646 0.0000936 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884873 rs34342646 0.00958 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884873 rs34342646 0.0125 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884873 rs34342646 1.17E-15 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44884873 rs34342646 4.17E-40 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44884873 rs34342646 5.54E-16 PVRL2 NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884873 rs34342646 5.87E-10 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44884873 rs34342646 7.99E-11 NR NR NR NR NA NECTIN2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44886339 rs7254892 0.0000112 PVRL2 NR NR NR NA NECTIN2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44887076 rs283815 0.000000307 PVRL2 A A 0.7 NA NECTIN2 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic HRS 9424 All Age at onset Other intron_variant chr19 44887076 rs283815 1.41E-08 PVRL2 G G 1.5 1.5 NECTIN2 SNP-based Disease risk 29107063 Multi-ethnic HRS 9424 All AD AD intron_variant chr19 44888997 rs6857 0.000000446 PVRL2 T T 1.37 1.37 NECTIN2 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD 3_prime_UTR_variant chr19 44888997 rs6857 0.000000498 PVRL2 T T 1.5 1.5 NECTIN2 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD 3_prime_UTR_variant chr19 44888997 rs6857 0.000000703 PVRL2 T T 1.31 1.31 NECTIN2 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD 3_prime_UTR_variant chr19 44888997 rs6857 0.000032 PVRL2 T T 1.23 1.23 NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD 3_prime_UTR_variant chr19 44888997 rs6857 0.0026 PVRL2 T T NR NA NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD 3_prime_UTR_variant chr19 44888997 rs6857 0.0063 PVRL2 T T 1.22 1.22 NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD 3_prime_UTR_variant chr19 44888997 rs6857 0.0063 PVRL2 T T NR NA NECTIN2 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD 3_prime_UTR_variant chr19 44888997 rs6857 1.49E-108 PVRL2 T T 3.23 3.23 NECTIN2 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD 3_prime_UTR_variant chr19 44888997 rs6857 1.78E-27 APOE T T 1.29 3.63279 NECTIN2 SNP-based Endophenotype 25188341 Caucasian ADGC 4046 All Neuritic Plaque Neuropathology 3_prime_UTR_variant chr19 44888997 rs6857 2.02E-62 APOE T T 1.61 5.00281 NECTIN2 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology 3_prime_UTR_variant chr19 44888997 rs6857 2.21E-12 PVRL2 T T 1.34 1.34 NECTIN2 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD 3_prime_UTR_variant chr19 44888997 rs6857 2.92E-21 APOE T T 0.67 1.95424 NECTIN2 SNP-based Endophenotype 25188341 Caucasian ADGC 2807 All Cerebral amyloid angiopathy (CAA Neuropathology 3_prime_UTR_variant chr19 44888997 rs6857 3.14E-47 APOE T T 0.95 2.58571 NECTIN2 SNP-based Endophenotype 25188341 Caucasian ADGC 4232 All "Neuritic Plaque (Ordinal, 4 categories)" Neuropathology 3_prime_UTR_variant chr19 44888997 rs6857 3.48E-38 APOE T T 1.5 4.48169 NECTIN2 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology 3_prime_UTR_variant chr19 44888997 rs6857 4.73E-47 APOE T T 0.66 1.93479 NECTIN2 SNP-based Endophenotype 25188341 Caucasian ADGC 4707 All "NFT Braak (Ordinal I, 7 categories)" Neuropathology 3_prime_UTR_variant chr19 44888997 rs6857 4.83E-44 APOE T T 0.79 2.2034 NECTIN2 SNP-based Endophenotype 25188341 Caucasian ADGC 4735 All "NFT Braak (Ordinal II, 4 categories)" Neuropathology 3_prime_UTR_variant chr19 44891079 rs71352238 0.00000158 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44891079 rs71352238 0.00000319 TOMM40 T T 1.5 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic HRS 9424 All Age at onset Other intron_variant chr19 44891079 rs71352238 0.00000482 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr19 44891079 rs71352238 0.0000533 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44891079 rs71352238 0.00946 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44891079 rs71352238 0.0137 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44891079 rs71352238 1.13E-11 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44891079 rs71352238 1.78E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44891079 rs71352238 2.04E-10 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44891079 rs71352238 2.46E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44891079 rs71352238 5.68E-39 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44891079 rs71352238 7.54E-08 TOMM40 C C 1.6 1.6 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic HRS 9424 All AD AD intron_variant chr19 44892009 rs157580 0.00000684 TOMM40 NR NR NR NA TOMM40 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr19 44892009 rs157580 0.0000153 TOMM40 G G 0.49 0.49 TOMM40 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD intron_variant chr19 44892009 rs157580 0.0000643 TOMM40 G G NR NA TOMM40 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 44892009 rs157580 0.005 TOMM40 A A -0.34 0.71177 TOMM40 SNP-based Age at onset (AAO) / Survival 22869155 Caucasian ADGC 22771 All Age at onset Other intron_variant chr19 44892009 rs157580 0.13 TOMM40 A A 1.09 1.09 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44892009 rs157580 0.16 TOMM40 A A 1.05 1.05 TOMM40 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All LOAD AD intron_variant chr19 44892009 rs157580 1.22E-09 TOMM40 G G 0.66 0.66 TOMM40 SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD intron_variant chr19 44892009 rs157580 1.50E-23 TOMM40 G G 0.5 0.5 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic ADGC 4561 All AD AD intron_variant chr19 44892009 rs157580 2.77E-29 TOMM40 A A 1.7 1.7 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44892009 rs157580 2.79E-17 NR G G NR NA TOMM40 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr19 44892009 rs157580 3.87E-11 TOMM40 G G NR NA TOMM40 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 44892009 rs157580 7.78E-13 TOMM40 G G 0.63 0.63 TOMM40 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD intron_variant chr19 44892009 rs157580 8.24E-11 TOMM40 G G NR NA TOMM40 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr19 44892009 rs157580 9.60E-35 "PVRL2, TOMM40" G G 0.51 0.51 TOMM40 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44892009 rs157580 9.60E-54 TOMM40 NR NR 0.63 0.63 TOMM40 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr19 44892009 rs157580 <1.00E-06 EPC2 NR NR NR NA TOMM40 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44892362 rs2075650 0 TOMM40 NR NR NR NA TOMM40 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44892362 rs2075650 0.000000165 TOMM40 G G 1.5 1.5 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic HRS 9424 All AD AD intron_variant chr19 44892362 rs2075650 0.000000303 TOMM40 G G NR NA TOMM40 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intron_variant chr19 44892362 rs2075650 0.000000517 TOMM40 A A 1.5 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic HRS 9424 All Age at onset Other intron_variant chr19 44892362 rs2075650 0.000000822 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892362 rs2075650 0.00000125 TOMM40 A A 0.71 0.71 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44892362 rs2075650 0.00000167 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr19 44892362 rs2075650 0.0000146 TOMM40 A A 1.7 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Caucasian CHARGE 3651 All Age at onset Other intron_variant chr19 44892362 rs2075650 0.000064 TOMM40 A A 0.84 0.84 TOMM40 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44892362 rs2075650 0.0000882 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892362 rs2075650 0.0032 TOMM40 NR NR NR NA TOMM40 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr19 44892362 rs2075650 0.0034 TOMM40 A A NR NA TOMM40 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44892362 rs2075650 0.01 TOMM40 A A 0.85 0.85 TOMM40 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44892362 rs2075650 0.01 TOMM40 A A NR NA TOMM40 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD intron_variant chr19 44892362 rs2075650 0.0203 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892362 rs2075650 0.0224 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892362 rs2075650 0.16 TOMM40 A A 0.89 0.89 TOMM40 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All LOAD AD intron_variant chr19 44892362 rs2075650 0.31 TOMM40 A A 0.15 1.16183 TOMM40 SNP-based Age at onset (AAO) / Survival 22869155 Caucasian ADGC 22771 All Age at onset Other intron_variant chr19 44892362 rs2075650 1.01E-11 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892362 rs2075650 1.04E-295 APOE G G 2.53 2.53 TOMM40 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intron_variant chr19 44892362 rs2075650 1.18E-15 "APOC1, APOC4, APOE, PVRL2, TOMM40" A A NR NA TOMM40 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr19 44892362 rs2075650 1.22E-11 NR G G -0.049 0.952181 TOMM40 SNP-based Cognitive 23562540 NR ROSMAP 1593 All global cognitive decline Cognitive intron_variant chr19 44892362 rs2075650 1.30E-36 TOMM40 G G 2.96 2.96 TOMM40 SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD intron_variant chr19 44892362 rs2075650 1.70E-94 TOMM40 A A 0.35 0.35 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44892362 rs2075650 1.80E-157 TOMM40 NR NR 2.53 2.53 TOMM40 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr19 44892362 rs2075650 1.99E-15 TOMM40 A A 2.3 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic CHARGE 5018 All Age at onset Other intron_variant chr19 44892362 rs2075650 2.21E-39 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44892362 rs2075650 2.86E-64 TOMM40 G G 3.6 3.6 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic ADGC 4561 All AD AD intron_variant chr19 44892362 rs2075650 2.95E-81 "APOC1, APOC4, APOE, PVRL2, TOMM40" A A 0.35 NA TOMM40 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr19 44892362 rs2075650 3.18E-68 APOE G G 2.23 2.23 TOMM40 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intron_variant chr19 44892362 rs2075650 3.21E-73 "APOC1, APOC4, APOE, PVRL2, TOMM40" A A 0.35 NA TOMM40 SNP-based Disease risk 21379329 Caucasian ADGC 3446 Northwestern European ancestry LOAD AD intron_variant chr19 44892362 rs2075650 3.22E-11 TOMM40 NR NR NR NA TOMM40 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr19 44892362 rs2075650 3.74E-08 "APOC1, APOC4, APOE, PVRL2, TOMM40" A A 0.25 NA TOMM40 SNP-based Disease risk 21379329 Caucasian ADGC 214 Ashkenazi Jewish LOAD AD intron_variant chr19 44892362 rs2075650 3.88E-10 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892362 rs2075650 4.02E-09 TOMM40 G G 2.3 2.3 TOMM40 SNP-based Disease risk 29107063 Caucasian CHARGE 3651 All AD AD intron_variant chr19 44892362 rs2075650 4.28E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892362 rs2075650 4.67E-172 APOE G G 2.61 2.61 TOMM40 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intron_variant chr19 44892362 rs2075650 4.87E-36 TOMM40 G G 2.94 2.94 TOMM40 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD intron_variant chr19 44892362 rs2075650 5.81E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892362 rs2075650 6.22E-184 NR G G 0.985 2.67781 TOMM40 SNP-based Disease risk 23562540 Caucasian ADGC 22771 All AD AD intron_variant chr19 44892362 rs2075650 6.24E-14 APOE NR NR 2.03 2.03 TOMM40 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr19 44892362 rs2075650 6.24E-14 TOMM40 G G 5.72 5.72 TOMM40 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD intron_variant chr19 44892362 rs2075650 8.54E-116 "PVRL2, TOMM40" G G 4.48 4.48 TOMM40 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44892362 rs2075650 9.32E-15 TOMM40 G G 2.3 2.3 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic CHARGE 5018 All AD AD intron_variant chr19 44892362 rs2075650 9.33E-10 NR G G 0.266 1.30474 TOMM40 SNP-based Neuropathology 23562540 NR ROSMAP 651 All tangle counts Neuropathology intron_variant chr19 44892362 rs2075650 <1.00E-06 EPC2 NR NR NR NA TOMM40 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44892362 rs2075650 <1.00E-06 EPC2 NR NR NR NA TOMM40 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF P-tau181p/Ab1-42 Fluid biomarker intron_variant chr19 44892362 rs2075650 <1.00E-06 EPC2 NR NR NR NA TOMM40 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau/Ab1-42 Fluid biomarker intron_variant chr19 44892457 rs157581 0.85 APOE NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD synonymous_variant chr19 44892457 rs157581 1.30E-46 APOE NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD synonymous_variant chr19 44892457 rs157581 1.60E-51 APOE NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD synonymous_variant chr19 44892457 rs157581 2.94E-15 TOMM40 NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD synonymous_variant chr19 44892457 rs157581 3.38E-14 TOMM40 NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD synonymous_variant chr19 44892457 rs157581 4.80E-55 APOE NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD synonymous_variant chr19 44892457 rs157581 4.82E-24 TOMM40 NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD synonymous_variant chr19 44892457 rs157581 5.18E-22 TOMM40 NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD synonymous_variant chr19 44892457 rs157581 6.86E-14 TOMM40 NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD synonymous_variant chr19 44892457 rs157581 7.10E-59 APOE NR NR NR NA TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD synonymous_variant chr19 44892457 rs157581 <1.00E-08 TOMM40 NR NR 2.73 2.73 TOMM40 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD synonymous_variant chr19 44892652 rs34404554 0.00000172 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892652 rs34404554 0.00000544 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr19 44892652 rs34404554 0.0000291 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892652 rs34404554 0.0134 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892652 rs34404554 0.0143 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892652 rs34404554 1.01E-39 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44892652 rs34404554 1.33E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892652 rs34404554 1.87E-12 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44892652 rs34404554 3.19E-10 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892652 rs34404554 3.58E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44892887 rs11556505 0.00000158 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker synonymous_variant chr19 44892887 rs11556505 0.00000572 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker synonymous_variant chr19 44892887 rs11556505 0.0000386 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker synonymous_variant chr19 44892887 rs11556505 0.0155 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker synonymous_variant chr19 44892887 rs11556505 0.0177 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker synonymous_variant chr19 44892887 rs11556505 1.06E-39 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker synonymous_variant chr19 44892887 rs11556505 1.68E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker synonymous_variant chr19 44892887 rs11556505 2.83E-12 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker synonymous_variant chr19 44892887 rs11556505 3.00E-10 NR NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker synonymous_variant chr19 44892887 rs11556505 3.48E-16 TOMM40 NR NR NR NA TOMM40 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker synonymous_variant chr19 44892962 rs157582 0.000000168 TOMM40 C C 0.7 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic HRS 9424 All Age at onset Other intron_variant chr19 44892962 rs157582 0.00000326 TOMM40 T T 1.6 1.6 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44892962 rs157582 0.0011 TOMM40 T T 1.3 1.3 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44892962 rs157582 0.222 TOMM40 T T 1.15 1.15 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44892962 rs157582 2.54E-91 TOMM40 T T 2.73 2.73 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44892962 rs157582 3.32E-09 TOMM40 T T 1.5 1.5 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic HRS 9424 All AD AD intron_variant chr19 44893416 rs157583 0.0000248 TOMM40 T T 2.08 2.08 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44893416 rs157583 0.7 TOMM40 T T 0.92 0.92 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44896639 rs76366838 1.71E-08 TOMM40 G G 0.4 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic HRS 9424 All Age at onset Other intron_variant chr19 44898409 rs8106922 0.0000454 TOMM40 G G 0.7 0.7 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic CHARGE 5018 All AD AD intron_variant chr19 44898409 rs8106922 0.0000834 TOMM40 A A 0.7 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic CHARGE 5018 All Age at onset Other intron_variant chr19 44898409 rs8106922 0.0000973 TOMM40 A A 1.48 1.48 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44898409 rs8106922 0.108 TOMM40 G G 0.79 0.79 TOMM40 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD intron_variant chr19 44898409 rs8106922 0.144 TOMM40 A A 1.18 1.18 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44898409 rs8106922 0.23 TOMM40 A A 0.15 1.16183 TOMM40 SNP-based Age at onset (AAO) / Survival 22869155 Caucasian ADGC 22771 All Age at onset Other intron_variant chr19 44898409 rs8106922 0.36 TOMM40 A A 0.97 0.97 TOMM40 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All LOAD AD intron_variant chr19 44898409 rs8106922 0.679 TOMM40 A A 1.02 1.02 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44898409 rs8106922 1.14E-23 TOMM40 G G 0.5 0.5 TOMM40 SNP-based Disease risk 29107063 Multi-ethnic ADGC 4561 All AD AD intron_variant chr19 44898409 rs8106922 1.17E-25 TOMM40 G G 0.57 0.57 TOMM40 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 44898409 rs8106922 1.21E-10 TOMM40 G G NR NA TOMM40 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr19 44898409 rs8106922 2.06E-28 TOMM40 A A 1.66 1.66 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44898409 rs8106922 2.94E-12 TOMM40 G G 0.62 0.62 TOMM40 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD intron_variant chr19 44898409 rs8106922 3.10E-12 TOMM40 G G 0.62 0.62 TOMM40 SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD intron_variant chr19 44898409 rs8106922 3.96E-14 TOMM40 G G NR NA TOMM40 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 44898409 rs8106922 5.40E-39 TOMM40 NR NR 0.68 0.68 TOMM40 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr19 44898409 rs8106922 5.89E-09 TOMM40 G G NR NA TOMM40 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr19 44899959 rs115881343 2.03E-09 TOMM40 C C 0.5 NA TOMM40 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic HRS 9424 All Age at onset Other intron_variant chr19 44900155 rs1160985 0.0000492 TOMM40 T T 0.65 0.65 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44900155 rs1160985 0.326 TOMM40 T T 0.95 0.95 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44900155 rs1160985 0.73 TOMM40 T T 1.04 1.04 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr19 44900155 rs1160985 2.78E-33 TOMM40 T T 0.58 0.58 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD intron_variant chr19 44901322 rs394819 8.40E-11 "APOE, TOMM40" T T 1.89 1.89 TOMM40 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD missense_variant chr19 44903416 rs10119 0.000000595 TOMM40 A A 1.8 1.8 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD 3_prime_UTR_variant chr19 44903416 rs10119 0.0051 TOMM40 A A 1.22 1.22 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD 3_prime_UTR_variant chr19 44903416 rs10119 0.614 TOMM40 A A 1.07 1.07 TOMM40 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD 3_prime_UTR_variant chr19 44903416 rs10119 8.15E-70 TOMM40 A A 2.48 2.48 TOMM40 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD 3_prime_UTR_variant chr19 44905579 rs405509 0.000000098 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.00000131 APOE T T 1.5 1.5 APOE SNP-based Disease risk 29107063 Multi-ethnic CHARGE 5018 All AD AD upstream_gene_variant chr19 44905579 rs405509 0.00000477 APOE G G NR NA APOE SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.00000733 APOE G G NR NA APOE SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.0000116 APOE T T 1.4 NA APOE SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic CHARGE 5018 All Age at onset Other upstream_gene_variant chr19 44905579 rs405509 0.0000125 APOE NR NR NR NA APOE SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD upstream_gene_variant chr19 44905579 rs405509 0.0000125 APOE T T 1.18 1.18 APOE SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD upstream_gene_variant chr19 44905579 rs405509 0.0000598 APOE T T 1.15 1.15 APOE SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD upstream_gene_variant chr19 44905579 rs405509 0.000081 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.0001 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.0003 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.0013 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.002 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.00342 APOE C C 0.65 0.65 APOE SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.0035 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.43 APOE T T 0.97 0.97 APOE SNP-based Disease risk 22869155 Caucasian ADGC 22771 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.62 APOE T T 0.07 1.07251 APOE SNP-based Age at onset (AAO) / Survival 22869155 Caucasian ADGC 22771 All Age at onset Other upstream_gene_variant chr19 44905579 rs405509 0.74 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 0.93 APOE T T 1 1 APOE SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD upstream_gene_variant chr19 44905579 rs405509 1.47E-13 APOE C C 0.62 0.62 APOE SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 1.50E-20 APOE T T 1.7 1.7 APOE SNP-based Disease risk 29107063 Multi-ethnic ADGC 4561 All AD AD upstream_gene_variant chr19 44905579 rs405509 1.90E-13 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 2.08E-09 APOE G G NR NA APOE SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 2.29E-27 "APOE, TOMM40" G G 0.57 0.57 APOE SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD upstream_gene_variant chr19 44905579 rs405509 4.35E-73 APOE NR NR NR NA APOE SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr19 44905579 rs405509 4.40E-12 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 4.90E-37 APOE NR NR 0.7 0.7 APOE SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD upstream_gene_variant chr19 44905579 rs405509 8.13E-14 APOE C C 0.61 0.61 APOE SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD upstream_gene_variant chr19 44905579 rs405509 <1.00E-08 APOE NR NR 1.43 1.43 APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD upstream_gene_variant chr19 44906745 rs769449 0.000000958 APOE NR NR NR NA APOE SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr19 44906745 rs769449 0.00000639 NR NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 0.0000322 NR NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 0.00907 NR NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 0.0129 NR NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 0.0842 GLIS1 A A 0.08 1.08329 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1530 All AD Progression (based on CDR Score) Cognitive intron_variant chr19 44906745 rs769449 1.04E-10 NR NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 1.23E-12 NR NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 1.95E-16 APOE NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 2.56E-18 APOE NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 3.00E-12 APOE A A 1.9 1.9 APOE SNP-based Disease risk 29107063 Multi-ethnic HRS 9424 All AD AD intron_variant chr19 44906745 rs769449 3.12E-08 APOE G G 1.7 NA APOE SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic HRS 9424 All Age at onset Other intron_variant chr19 44906745 rs769449 3.29E-53 GLIS1 NR NR 0.11 1.11628 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF Ab1-42 Fluid biomarker intron_variant chr19 44906745 rs769449 4.05E-29 GLIS1 A A 0.08 1.08329 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 4.05E-29 GLIS1 NR NR 0.08 1.08329 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 4.31E-22 GLIS1 NR NR 0.09 1.09417 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 4.41E-12 GLIS1 NR NR 0.07 1.07251 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 4.78E-94 GLIS1 A A 0.101 1.10628 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44906745 rs769449 4.78E-94 GLIS1 NR NR 0.1 1.10517 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44906745 rs769449 5.30E-33 GLIS1 A A 0.08 1.08329 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 5.30E-33 GLIS1 NR NR 0.08 1.08329 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 5.58E-20 GLIS1 NR NR 0.09 1.09417 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF T-tau Fluid biomarker intron_variant chr19 44906745 rs769449 5.83E-14 GLIS1 NR NR 0.07 1.07251 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF P-tau181p Fluid biomarker intron_variant chr19 44906745 rs769449 6.76E-43 GLIS1 NR NR 0.09 1.09417 APOE SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF Ab1-42 Fluid biomarker intron_variant chr19 44906745 rs769449 6.81E-106 GLIS1 A A 0.72 2.05443 APOE SNP-based Age at onset (AAO) / Survival 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 39855 AD subjects Age at onset Other intron_variant chr19 44906745 rs769449 9.02E-47 APOE NR NR NR NA APOE SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr19 44906745 rs769449 9.86E-523 GLIS1 A A 3.52 33.7844 APOE SNP-based Disease risk 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 74046 All AD risk AD intron_variant chr19 44907187 rs769450 0.000159 APOE A A 0.7 0.7 APOE SNP-based Disease risk 29107063 Multi-ethnic CHARGE 5018 All AD AD intron_variant chr19 44908684 rs429358 0.00000059 NR e4 e4 -0.33 0.718924 APOE SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 167 AD subjects CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 0.0000061 NR e4 e4 -0.51 0.600496 APOE SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 113 AD subjects CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 0.000011 NR NR NR -0.7 0.496585 APOE SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 0.0000124 NR NR NR 4.82 4.82 APOE SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD missense_variant chr19 44908684 rs429358 0.0000823 NR NR NR 2.91 2.91 APOE SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD missense_variant chr19 44908684 rs429358 0.00502 APOE A A 0.83 NA APOE SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other missense_variant chr19 44908684 rs429358 0.01 NR e4 e4 -0.39 0.677057 APOE SNP-based Endophenotype 25027320 Caucasian ADNI 83 AD subjects CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 1.10E-12 APOE C C -0.5 0.606531 APOE SNP-based Endophenotype 25188341 Caucasian ADGC 3525 All "Lewy Body (Ordinal I, 5 categories)" Neuropathology missense_variant chr19 44908684 rs429358 1.2E-881 APOE C C 3.32 3.32 APOE SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD missense_variant chr19 44908684 rs429358 1.60E-79 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908684 rs429358 1.80E-10 NR NR NR 1.08 2.94468 APOE SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 2.20E-74 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908684 rs429358 2.60E-97 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908684 rs429358 2.83E-11 APOE C C -0.49 0.612626 APOE SNP-based Endophenotype 25188341 Caucasian ADGC 3526 All Lewy Body Neuropathology missense_variant chr19 44908684 rs429358 2.90E-79 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908684 rs429358 3.90E-43 APOE NR NR 2.39 2.39 APOE SNP-based Disease risk 30979435 Caucasian ADGC 6212 Age >=80 y AD AD missense_variant chr19 44908684 rs429358 4.30E-17 NR NR NR -0.4 0.67032 APOE SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 4.30E-17 NR e4 e4 -0.4 0.67032 APOE SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 4.50E-35 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908684 rs429358 4.87E-12 APOE C C -0.51 0.600496 APOE SNP-based Endophenotype 25188341 Caucasian ADGC 3526 All "Lewy Body (Ordinal II, 3 categories)" Neuropathology missense_variant chr19 44908684 rs429358 4.90E-286 APOE NR NR 3.93 3.93 APOE SNP-based Disease risk 30979435 Caucasian ADGC 13641 Age 60-79 y AD AD missense_variant chr19 44908684 rs429358 7.27E-30 APOE NR NR -0.13 0.878095 APOE SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma APOE Fluid biomarker missense_variant chr19 44908684 rs429358 <1.00E-06 EPC2 NR NR NR NA APOE SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 <1.00E-06 EPC2 NR NR NR NA APOE SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF P-tau181p Fluid biomarker missense_variant chr19 44908684 rs429358 <1.00E-06 EPC2 NR NR NR NA APOE SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF P-tau181p/Ab1-42 Fluid biomarker missense_variant chr19 44908684 rs429358 <1.00E-06 EPC2 NR NR NR NA APOE SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau/Ab1-42 Fluid biomarker missense_variant chr19 44908822 rs7412 0.0000021 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908822 rs7412 0.00023 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908822 rs7412 0.3 NR NR NR 0.52 0.52 APOE SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD missense_variant chr19 44908822 rs7412 0.753 NR NR NR 0.8 0.8 APOE SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD missense_variant chr19 44908822 rs7412 2.60E-13 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908822 rs7412 3.90E-11 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44908822 rs7412 4.10E-12 APOE NR NR NR NA APOE SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44910319 rs75627662 9.51E-296 APOE G G NR NA APOE SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD upstream_gene_variant chr19 44911194 rs439401 0.000000423 LOC100129500 A A 0.33 0.33 APOE SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD upstream_gene_variant chr19 44911194 rs439401 0.0000897 APOE T T NR NA APOE SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD upstream_gene_variant chr19 44911194 rs439401 0.11 NR T T 0.2 1.2214 APOE SNP-based Age at onset (AAO) / Survival 22869155 Caucasian ADGC 22771 All Age at onset Other upstream_gene_variant chr19 44911194 rs439401 0.16 NR T T 0.95 0.95 APOE SNP-based Disease risk 22869155 Caucasian ADGC 22771 All LOAD AD upstream_gene_variant chr19 44911194 rs439401 1.76E-09 LOC100129500 A A 0.66 0.66 APOE SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD upstream_gene_variant chr19 44911194 rs439401 3.80E-12 LOC100129500 A A 0.63 0.63 APOE SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD upstream_gene_variant chr19 44911194 rs439401 5.17E-17 "APOC1, APOE" T T 0.6 0.6 APOE SNP-based Disease risk 29107063 Multi-ethnic ADGC 4561 All AD AD upstream_gene_variant chr19 44911194 rs439401 7.97E-09 APOE T T NR NA APOE SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD upstream_gene_variant chr19 44911194 rs439401 8.82E-29 "APOC1, APOE" T T 0.54 0.54 APOE SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD upstream_gene_variant chr19 44911194 rs439401 9.15E-11 APOE T T NR NA APOE SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD upstream_gene_variant chr19 44911194 rs439401 <1.00E-06 EPC2 NR NR NR NA APOE SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF Ab1-42 Fluid biomarker upstream_gene_variant chr19 44912383 rs445925 0.000302 APOC1 A A 1.57 1.57 APOC1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD upstream_gene_variant chr19 44912383 rs445925 0.00079 APOE/APOC1 A A NR NA APOC1 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44912383 rs445925 0.25 "APOC1, APOE" A A 0.93 0.93 APOC1 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44912383 rs445925 0.443 APOC1 A A 1.13 1.13 APOC1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD upstream_gene_variant chr19 44912383 rs445925 0.47 APOE/APOC1 A A NR NA APOC1 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44912383 rs445925 4.10E-11 "APOC1, APOE" A A 0.74 0.74 APOC1 SNP-based Disease risk 22869155 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr19 44917997 rs12721046 2.39E-14 APOC1 G G 2.2 NA APOC1 SNP-based Age at onset (AAO) / Survival 29107063 Multi-ethnic CHARGE 5018 All Age at onset Other intron_variant chr19 44917997 rs12721046 2.93E-09 APOC1 G G 2 NA APOC1 SNP-based Age at onset (AAO) / Survival 29107063 Caucasian CHARGE 3651 All Age at onset Other intron_variant chr19 44917997 rs12721046 4.87E-09 APOC1 A A 2.2 2.2 APOC1 SNP-based Disease risk 29107063 Caucasian CHARGE 3651 All AD AD intron_variant chr19 44919689 rs4420638 0.000000154 APOC1 A A 0.61 0.61 APOC1 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 0.00000211 "APOC1, APOE, TOMM40" NR NR 0.28 0.28 APOC1 SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 0.0000132 "APOC1, APOE, TOMM40" NR NR NR NA APOC1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other downstream_gene_variant chr19 44919689 rs4420638 0.0247 "APOC1, APOE, TOMM40" NR NR 0.7 2.01375 APOC1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other downstream_gene_variant chr19 44919689 rs4420638 0.983 "APOC1, APOE, TOMM40" NR NR -0.05 0.951229 APOC1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other downstream_gene_variant chr19 44919689 rs4420638 1.07E-144 APOC1 A A 0.23 0.23 APOC1 SNP-based Disease risk 22159054 Caucasian "ADGC, CHARGE, GenADA" 9773 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 1.11E-12 "APOC1, APOE, TOMM40" NR NR NR NA APOC1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other downstream_gene_variant chr19 44919689 rs4420638 1.49E-17 APOE G G 0.35 1.41907 APOC1 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic Plaque Pathologic Burden Neuropathology downstream_gene_variant chr19 44919689 rs4420638 1.72E-51 "APOC1, APOE, TOMM40" NR NR 0.21 0.21 APOC1 SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 1.97E-42 "APOC1, APOE, TOMM40" NR NR 0.32 0.32 APOC1 SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 1.99E-11 "APOC1, APOE, TOMM40" NR NR NR NA APOC1 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 4.14E-14 "APOC1, APOE, TOMM40" NR NR 2.2 9.02501 APOC1 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other downstream_gene_variant chr19 44919689 rs4420638 6.44E-22 "APOC1, APOE, TOMM40" NR NR 0.38 0.38 APOC1 SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 7.38E-38 "APOC1, APOE, TOMM40" NR NR 0.25 0.25 APOC1 SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD downstream_gene_variant chr19 44919689 rs4420638 7.91E-149 "APOC1, APOE, TOMM40" NR NR 0.29 0.29 APOC1 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD downstream_gene_variant chr19 44944779 rs1132899 0.000017 APOE NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44944779 rs1132899 0.000028 APOE NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44944779 rs1132899 0.000076 APOC2 NR NR 1.19 1.19 APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD missense_variant chr19 44944779 rs1132899 0.00019 APOE NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44944779 rs1132899 0.0049 APOE NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44944779 rs1132899 0.0075 APOC2 NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD missense_variant chr19 44944779 rs1132899 0.013 APOC2 NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD missense_variant chr19 44944779 rs1132899 0.056 APOC2 NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD missense_variant chr19 44944779 rs1132899 0.13 APOE NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 2724 All LOAD AD missense_variant chr19 44944779 rs1132899 0.137 APOC2 NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD missense_variant chr19 44944779 rs1132899 0.975 APOC2 NR NR NR NA APOC4 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD missense_variant chr19 44946027 rs2288911 6.42E-10 APOC2 NR NR NR NA APOC4-APOC2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD 5_prime_UTR_variant chr19 44954978 rs41334244 5.01E-09 NR NR NR NR NA CLPTM1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD 5_prime_UTR_variant chr19 44979627 rs7257916 3.53E-08 CLPTM1 NR NR NR NA CLPTM1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 44984163 rs16979600 4.36E-11 CLPTM1 NR NR NR NA CLPTM1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 45040529 rs1560725 4.72E-08 SFRS16 NR NR NR NA CLASRP SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 45086337 rs1469704 0.0000126 GEMIN7 NR NR NR NA GEMIN7 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 45187631 rs12460985 3.21E-08 "BL0C1S3, EXOC3L2" NR NR NR NA MARK4 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD 5_prime_UTR_variant chr19 45205500 rs2627641 1.26E-13 "BL0C1S3, EXOC3L2" NR NR NR NA MARK4 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 45205630 rs597668 0.00000216 EXOC3L2 C C 1.18 1.18 MARK4 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intron_variant chr19 45205630 rs597668 0.000591 EXOC3L2 C C 1.18 1.18 MARK4 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intron_variant chr19 45205630 rs597668 0.00823 EXOC3L2 C C 0.88 0.88 MARK4 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr19 45205630 rs597668 0.01 EXOC3L2 NR NR 1.26 1.26 MARK4 SNP-based Disease risk 20460622 Caucasian Cohort from Europe 2349 All AD AD intron_variant chr19 45205630 rs597668 0.59 "EXOC3L2, BLOC1S3, MARK4" NR NR 1.04 1.04 MARK4 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr19 45205630 rs597668 0.731 EXOC3L2 C C 0.97 0.97 MARK4 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr19 45205630 rs597668 6.45E-09 EXOC3L2 C C 1.17 1.17 MARK4 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intron_variant chr19 45222848 rs10422797 0.00000102 EXOC3L2 C C 1.82 1.82 MARK4 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 45224865 rs10410003 0.00000311 EXOC3L2 NR NR NR NA MARK4 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD synonymous_variant chr19 45226017 rs346763 0.000000367 EXOC3L2 A A 1.8 1.8 MARK4 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr19 45595627 rs10405576 1.10E-26 GPR4 NR NR -1.35 0.25924 OPA3 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD GPR4 expression in Cerebellar Expression intron_variant chr19 45595627 rs10405576 1.39E-58 GPR4 NR NR -1.53 0.216536 OPA3 SNP-based eQTL 22685416 Caucasian MAYO 399 All GPR4 expression in Temporal cortex Expression intron_variant chr19 45595627 rs10405576 2.16E-28 GPR4 NR NR -1.27 0.280832 OPA3 SNP-based eQTL 22685416 Caucasian MAYO 197 AD GPR4 expression in Cerebellar Expression intron_variant chr19 45595627 rs10405576 2.56E-62 GPR4 NR NR -1.32 0.267135 OPA3 SNP-based eQTL 22685416 Caucasian MAYO 374 All GPR4 expression in Cerebellar Expression intron_variant chr19 45698914 rs2287019 0.123 NR C C 0.923 0.923 QPCTL SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr19 45698914 rs2287019 0.243 NR C C 0.949 0.949 QPCTL SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr19 45698914 rs2287019 0.42 NR C C 0 1 QPCTL SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr19 45698914 rs2287019 0.949 NR C C 0.998 0.998 QPCTL SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr19 45738583 rs76320948 0.0000154 AC074212.3 T T NR NA BHMG1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr19 45738583 rs76320948 0.000018 AC074212.3 T T NR NA BHMG1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr19 45738583 rs76320948 4.64E-08 AC074212.3 T T 5.46 NA BHMG1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr19 45772798 rs16939 0.0000464 DMPK NR NR NR NA DMPK SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 45842628 rs16980051 0.00000661 SYMPK NR NR NR NA SYMPK SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr19 45842628 rs16980051 0.00000661 SYMPK T T NR NA SYMPK SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD intron_variant chr19 45842628 rs16980051 0.000933 SYMPK T T NR NA SYMPK SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 51009 All Crohn disease Non-ADRD intron_variant chr19 47065746 rs3810291 0.083 NR A A 0.948 0.948 ZC3H4 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD 3_prime_UTR_variant chr19 47065746 rs3810291 0.19 NR A A 0.942 0.942 ZC3H4 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD 3_prime_UTR_variant chr19 47065746 rs3810291 0.294 NR A A 0 1 ZC3H4 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive 3_prime_UTR_variant chr19 47065746 rs3810291 0.589 NR A A 1.02 1.02 ZC3H4 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD 3_prime_UTR_variant chr19 51224706 rs3865444 0.000000051 CD33 A A 0.91 0.91 CD33 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.000000107 CD33 A A 0.89 0.89 CD33 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.000000201 CD33 A A 0.89 0.89 CD33 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.00000082 CD33 A A 0.88 0.88 CD33 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.00000189 CD33 A A 0.88 0.88 CD33 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.000003 CD33 A A 0.94 0.94 CD33 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.0000196 CD33 NR NR -0.255 0.774916 CD33 SNP-based eQTL 30448613 Caucasian UKBEC 49 All IER2 (t3822216) expression in temporal cortex Expression upstream_gene_variant chr19 51224706 rs3865444 0.0000497 CD33 A A NR NA CD33 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD upstream_gene_variant chr19 51224706 rs3865444 0.00022 CD33 NR NR 0.89 0.89 CD33 SNP-based Disease risk 21460840 Caucasian "EADI, GERAD" 13448 All AD AD upstream_gene_variant chr19 51224706 rs3865444 0.000449 CD33 NR NR 0.91 0.91 CD33 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD upstream_gene_variant chr19 51224706 rs3865444 0.002 CD33 NR NR 0.92 0.92 CD33 SNP-based Disease risk 21460841 Caucasian "CHARGE, EADI, GERAD" 25818 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.008 CD33 A A 0.87 0.87 CD33 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.015 CD33 A A 0.87 0.87 CD33 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.016 CD33 A A 0.86 0.86 CD33 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology upstream_gene_variant chr19 51224706 rs3865444 0.0213 CD33 A A 0.91 0.91 CD33 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.026 CD33 A A 0.84 0.84 CD33 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology upstream_gene_variant chr19 51224706 rs3865444 0.0293 CD33 A A 0.92 0.92 CD33 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.174 NR A A -0.04 0.960789 CD33 SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology upstream_gene_variant chr19 51224706 rs3865444 0.206 CD33 A A 1.09 NA CD33 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other upstream_gene_variant chr19 51224706 rs3865444 0.338 CD33 A A 0.13 1.13883 CD33 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other upstream_gene_variant chr19 51224706 rs3865444 0.377 CD33 A A 0.1 1.10517 CD33 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other upstream_gene_variant chr19 51224706 rs3865444 0.492 CD33 A A 1.04 1.04 CD33 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.69 CD33 A A 0.99 0.99 CD33 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 0.69 CD33 NR NR 0.95 0.95 CD33 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging upstream_gene_variant chr19 51224706 rs3865444 0.732 CD33 A A 0.95 0.95 CD33 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 1.60E-09 CD33 NR NR 0.91 0.91 CD33 SNP-based Disease risk 21460840 Caucasian "ADGC, GERAD" NR All AD AD upstream_gene_variant chr19 51224706 rs3865444 1.60E-09 CD33 NR NR 0.91 0.91 CD33 SNP-based Disease risk 21460841 Caucasian "ADGC, CHARGE, EADI, GERAD" 48589 All LOAD AD upstream_gene_variant chr19 51224706 rs3865444 4.25E-08 CD33 A A NR NA CD33 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD upstream_gene_variant chr19 51224706 rs3865444 6.34E-09 CD33 A A -5.81 NA CD33 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD upstream_gene_variant chr19 51224706 rs3865444 NR CD33 C C 1.26 1.26 CD33 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD upstream_gene_variant chr19 51224706 rs3865444 NR ZCWPW1 C C 1.28 1.28 CD33 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD upstream_gene_variant chr19 51224706 rs3865444 NR ZCWPW1 C C 1.44 1.44 CD33 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD upstream_gene_variant chr19 51225221 rs12459419 0.000402 CD33 NR NR 0.91 0.91 CD33 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD missense_variant chr19 51293865 rs10419982 0.00054 CD33 A A 1.38 1.38 IGLON5 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr19 55051034 rs6509916 0.00000583 RDH13 G G 1.34 1.34 RDH13 SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD intron_variant chr19 55051034 rs6509916 0.0223 RDH13 G G 0.87 0.87 RDH13 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD intron_variant chr19 55051034 rs6509916 0.0334 RDH13 G G 1.1 1.1 RDH13 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD intron_variant chr19 56182251 rs3745833 0.00005 GALP NR NR 1.2 1.2 GALP SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD splice_region_variant&synonymous_variant chr19 56182251 rs3745833 0.008 GALP NR NR NR NA GALP SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD splice_region_variant&synonymous_variant chr19 56182251 rs3745833 0.036 GALP NR NR NR NA GALP SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD splice_region_variant&synonymous_variant chr19 56182251 rs3745833 0.061 GALP NR NR NR NA GALP SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD splice_region_variant&synonymous_variant chr19 56182251 rs3745833 0.261 GALP NR NR NR NA GALP SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD splice_region_variant&synonymous_variant chr19 56182251 rs3745833 0.512 GALP NR NR NR NA GALP SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD splice_region_variant&synonymous_variant chr19 58262705 rs260462 1.88E-125 ZNF544 NR NR -1.3 0.272532 ZNF544 SNP-based eQTL 22685416 Caucasian MAYO 399 All ZNF544 expression in Temporal cortex Expression missense_variant chr19 58262705 rs260462 3.19E-48 ZNF544 NR NR -1.21 0.298197 ZNF544 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD ZNF544 expression in Cerebellar Expression missense_variant chr19 58262705 rs260462 3.67E-95 ZNF544 NR NR -1.16 0.313486 ZNF544 SNP-based eQTL 22685416 Caucasian MAYO 374 All ZNF544 expression in Cerebellar Expression missense_variant chr19 58262705 rs260462 7.79E-42 ZNF544 NR NR -1.12 0.32628 ZNF544 SNP-based eQTL 22685416 Caucasian MAYO 197 AD ZNF544 expression in Cerebellar Expression missense_variant chr2 622827 rs2867125 0.343 NR C C 0.973 0.973 TMEM18 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr2 622827 rs2867125 0.39 NR C C 1.051 1.051 TMEM18 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr2 622827 rs2867125 0.701 NR C C 0.982 0.982 TMEM18 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr2 622827 rs2867125 0.93 NR C C 0 1 TMEM18 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr2 5329700 rs6734151 0.872 NR NR NR NR NA SOX11 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intergenic_region chr2 10338810 rs4669573 0.00000367 "HPCAL1, ODC1" NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr2 10338810 rs4669573 0.0000526 "HPCAL1, ODC1" NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 10338810 rs4669573 0.000085 NR NR NR 1.64 1.64 HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr2 10338810 rs4669573 0.00118 NR NR NR 1.42 1.42 HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 10338810 rs4669573 0.00628 "HPCAL1, ODC1" NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr2 10338810 rs4669573 0.2504 "HPCAL1, ODC1" NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr2 10338810 rs4669573 0.3831 "HPCAL1, ODC1" NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr2 10338810 rs4669573 0.523 "HPCAL1, ODC1" NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr2 10338810 rs4669573 1 NR NR NR 1.11 1.11 HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr2 10345283 rs10197851 0.00000713 NR NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr2 10345283 rs10197851 0.000102 NR NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 10345283 rs10197851 0.00016 NR NR NR 0.62 0.62 HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr2 10345283 rs10197851 0.00221 NR NR NR 0.71 0.71 HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 10345283 rs10197851 0.0202 NR NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr2 10345283 rs10197851 0.10894 NR NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr2 10345283 rs10197851 0.543 NR NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr2 10345283 rs10197851 0.7171 NR NR NR NR NA HPCAL1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr2 10345283 rs10197851 1 NR NR NR 0.91 0.91 HPCAL1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr2 12731066 rs13408093 2.12E-25 TRIB2 NR NR NR NA TRIB2 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker intron_variant chr2 12731066 rs13408093 6.88E-10 TRIB2 NR NR NR NA TRIB2 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker intron_variant chr2 17246318 rs11889338 0.00000894 NR A A 1.55 1.55 RAD51AP2 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr2 17593765 rs4038131 0.00000059 VSNL1 NR NR 0.65 0.65 VSNL1 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intron_variant chr2 24935139 rs713586 0.018 NR C C 0.905 0.905 DNAJC27 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr2 24935139 rs713586 0.446 NR C C 0 1 DNAJC27 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr2 24935139 rs713586 0.46 NR C C 0.974 0.974 DNAJC27 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr2 24935139 rs713586 0.784 NR C C 1.01 1.01 DNAJC27 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr2 27684606 rs17006206 0.0000023 SLC4A1AP G G 2.05 2.05 SLC4A1AP SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr2 34687783 rs11683103 0.00000858 NR NR NR NR NA FAM98A SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr2 37237087 rs61208496 0.0000573 C20RF56 T T NR NA NDUFAF7 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr2 37237087 rs61208496 0.000188 C20RF56 T T NR NA NDUFAF7 SNP-based Cross phenotype 30413934 Caucasian "GIANT, UKBB" 180423 All Waist-to-hip ratio (WHR) Non-ADRD intron_variant chr2 37237087 rs61208496 0.00804 C20RF56 T T 1 1 NDUFAF7 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr2 43439852 rs7575024 0.0000026 THADA NR NR NR NA THADA SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr2 43459106 rs17030835 0.0000017 THADA NR NR NR NA THADA SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr2 43836592 rs72796734 0.0000233 ABCG5 T T NR NA ABCG5 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr2 43836592 rs72796734 0.000829 ABCG5 T T NR NA ABCG5 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr2 43836592 rs72796734 0.0132 ABCG5 T T 0.93 0.93 ABCG5 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr2 43836592 rs72796734 0.0326 ABCG5 T T 0.94 0.94 ABCG5 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr2 43836592 rs72796734 0.115 ABCG5 T T 0.84 0.84 ABCG5 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr2 43836592 rs72796734 0.624 ABCG5 T T 1 1 ABCG5 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr2 45751503 rs1456585679 0.0011 NR G G -0.18 0.83527 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker NA chr2 45775021 rs6753292 0.91 NR T T 0.01 1.01005 PRKCE SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr2 45797073 rs6720975 0.000029 PRKCE A A 1.61 5.00281 PRKCE SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 337 Probable AD Delta MMSE (annualized difference between MMSE score at baseline and at follow-up) Cognitive intron_variant chr2 45797073 rs6720975 0.000387 PRKCE A A 1.76 1.76 PRKCE SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 337 Probable AD "Responder (MMSE increased, remained stable, or the Delta MMSE fell by 1or less) vs Non-responder (worsening of >3 points in Delta MMSE)" Cognitive intron_variant chr2 45797073 rs6720975 0.000449 PRKCE A A 1.81 6.11045 PRKCE SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 169 Probable AD Delta MMSE (annualized difference between MMSE score at baseline and at follow-up) Cognitive intron_variant chr2 45797073 rs6720975 0.000514 PRKCE A A 2.19 2.19 PRKCE SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 169 Probable AD "Responder (MMSE increased, remained stable, or the Delta MMSE fell by 1or less) vs Non-responder (worsening of >3 points in Delta MMSE)" Cognitive intron_variant chr2 45797073 rs6720975 0.026 PRKCE A A 1.33 3.78104 PRKCE SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 168 Probable AD Delta MMSE (annualized difference between MMSE score at baseline and at follow-up) Cognitive intron_variant chr2 45797073 rs6720975 0.112 PRKCE A A 1.43 1.43 PRKCE SNP-based Endophenotype 23374588 Caucasian Cohort from Italy 168 Probable AD "Responder (MMSE increased, remained stable, or the Delta MMSE fell by 1or less) vs Non-responder (worsening of >3 points in Delta MMSE)" Cognitive intron_variant chr2 46886961 rs6715234 0.00000882 "MCFD2, LOC388948" NR NR NR NA MCFD2 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr2 47658337 rs2969775 0.00000211 AC079250.1 NR NR 0.68 0.68 MSH2 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intergenic_region chr2 50648741 rs858952 0.00000945 NRXN1 C C NR NA NRXN1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr2 50648741 rs858952 0.000222 NRXN1 C C NR NA NRXN1 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr2 50648741 rs858952 0.00308 NRXN1 C C 1.05 1.05 NRXN1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr2 50648741 rs858952 0.00769 NRXN1 C C 1.04 1.04 NRXN1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr2 50648741 rs858952 0.234 NRXN1 C C 1 1 NRXN1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr2 50648741 rs858952 0.467 NRXN1 C C 0.96 0.96 NRXN1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr2 53040635 rs77597338 0.000011 ASB3 NR NR NR NA ASB3 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intergenic_region chr2 53040635 rs77597338 0.0044 ASB3 NR NR NR NA ASB3 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intergenic_region chr2 53040635 rs77597338 0.0045 ASB3 NR NR NR NA ASB3 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intergenic_region chr2 53040635 rs77597338 0.025 ASB3 NR NR NR NA ASB3 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intergenic_region chr2 55925615 rs146896516 3.91E-12 NR A A 0.15 1.16183 EFEMP1 SNP-based Endophenotype 29752348 Caucasian UKBB 8429 All White Matter Hyperintensity Volume Imaging upstream_gene_variant chr2 57912830 rs140500963 0.0135 VRK2 NR NR NR NA VRK2 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr2 57912830 rs140500963 0.98402 NA NR NR NR NA VRK2 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr2 59046446 rs72804029 0.0000027 NR T T -0.8 0.449329 FANCL SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr2 59046446 rs72804029 0.01 NR T T -0.26 0.771052 FANCL SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr2 59046446 rs72804029 0.73 NR T T 0.04 1.04081 FANCL SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr2 59075742 rs887912 0.074 NR T T 1.083 1.083 FANCL SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr2 59075742 rs887912 0.508 NR T T 0.984 0.984 FANCL SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr2 59075742 rs887912 0.778 NR T T 0.989 0.989 FANCL SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr2 59075742 rs887912 0.791 NR T T 0.001 1.001 FANCL SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr2 60375757 rs243034 0.00000131 MIR4432 C C 1.52 1.52 BCL11A SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr2 61149328 rs720201 0.000694 C2orf74 C C NR NA C2orf74 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intron_variant chr2 61149328 rs720201 1.34E-164 NR C C NR NA C2orf74 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) C2orf74 (ILMN_1754501) expression Expression intron_variant chr2 61177796 rs2600667 0.000175 AHSA2 T T NR NA USP34 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD 5_prime_UTR_variant chr2 61177796 rs2600667 1.53E-22 NR T T NR NA USP34 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AHSA2 expression in Caudate basal ganglia Expression 5_prime_UTR_variant chr2 61177796 rs2600667 2.30E-15 NR T T NR NA USP34 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AHSA2 expression in Hypothalamus Expression 5_prime_UTR_variant chr2 61177796 rs2600667 2.65E-24 NR T T NR NA USP34 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AHSA2 expression in Nucleus accumbens Expression 5_prime_UTR_variant chr2 61177796 rs2600667 5.43E-13 NR T T NR NA USP34 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AHSA2 expression in Substantia nigra Expression 5_prime_UTR_variant chr2 61177796 rs2600667 6.30E-28 NR T T NR NA USP34 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AHSA2 expression in Cortex Expression 5_prime_UTR_variant chr2 61177796 rs2600667 7.23E-22 NR T T NR NA USP34 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AHSA2 expression in Putamen basal ganglia Expression 5_prime_UTR_variant chr2 61177796 rs2600667 9.79E-40 NR T T NR NA USP34 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AHSA2 expression in Cerebellum Expression 5_prime_UTR_variant chr2 64732197 rs12994639 0.0000953 SERTAD2 G G NR NA SERTAD2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr2 64732197 rs12994639 0.0016 SERTAD2 G G NR NA SERTAD2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr2 64732197 rs12994639 0.234 SERTAD2 G G 1 1 SERTAD2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr2 64839177 rs741477 0.0000305 NR G G NR NA SERTAD2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr2 64839177 rs741477 0.0000544 Intergenic (as reported in paper) G G NR NA SERTAD2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr2 64839177 rs741477 0.00124 NR G G NR NA SERTAD2 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr2 64855281 rs55819441 0.00014 AK097952 T T NR NA SERTAD2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr2 64855281 rs55819441 0.000956 AK097952 T T NR NA SERTAD2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr2 64855281 rs55819441 0.0755 AK097952 T T 0.96 0.96 SERTAD2 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr2 64855281 rs55819441 0.101 AK097952 T T 0.97 0.97 SERTAD2 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr2 64855281 rs55819441 0.627 AK097952 T T 1 1 SERTAD2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr2 64855281 rs55819441 0.635 AK097952 T T 1.05 1.05 SERTAD2 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr2 69138666 rs7561207 0.00000408 ANTXR1 A A 0.47 0.47 ANTXR1 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr2 73928514 rs7557705 0.00494 DGUOK T T NR NA DGUOK SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr2 73928514 rs7557705 3.29E-11 NR T T NR NA DGUOK SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group DGUOK (ILMN_2242403) expression Expression intron_variant chr2 88218921 rs7589728 0.00000495 THNSL2 NR NR NR NA THNSL2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr2 88595833 rs7571971 0.0703 RPIA NR NR -0.04 0.960789 EIF2AK3 SNP-based eQTL 22685416 Caucasian MAYO 374 All RPIA (ILMN_1714809) expression in Cerebellar Expression 5_prime_UTR_variant chr2 88595833 rs7571971 0.0957 RPIA NR NR -0.07 0.932394 EIF2AK3 SNP-based eQTL 22685416 Caucasian MAYO 98 PSP RPIA (ILMN_1714809) expression in Cerebellar Expression 5_prime_UTR_variant chr2 88595833 rs7571971 0.519 RPIA NR NR 0.03 1.03045 EIF2AK3 SNP-based eQTL 22685416 Caucasian MAYO 107 PSP RPIA (ILMN_1714809) expression in Temporal cortex Expression 5_prime_UTR_variant chr2 88595833 rs7571971 0.768 RPIA NR NR 0.01 1.01005 EIF2AK3 SNP-based eQTL 22685416 Caucasian MAYO 202 AD RPIA (ILMN_1714809) expression in Temporal cortex Expression 5_prime_UTR_variant chr2 88595833 rs7571971 0.921 RPIA NR NR 0 1 EIF2AK3 SNP-based eQTL 22685416 Caucasian MAYO 399 All RPIA (ILMN_1714809) expression in Temporal cortex Expression 5_prime_UTR_variant chr2 88595833 rs7571971 4.20E-13 EIF2AK3 NA NA 0.75 0.75 EIF2AK3 SNP-based Disease Risk 22685416 Caucasian "Cohorts from Europe, USA" 8851 All Progressive Supranuclear Palsy (PSP) ADRD 5_prime_UTR_variant chr2 100933381 rs3754675 0.0000057 NPAS2 C C NR NA NPAS2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr2 100933381 rs3754675 0.00003 NPAS2 C C NR NA NPAS2 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr2 100933381 rs3754675 0.0144 NPAS2 C C NR NA NPAS2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr2 106026098 rs34487851 0.00000002 ECRG4 NR NR NR NA ECRG4 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neuritic plaque (NP)+Neurofibrillary tangles (NFT) Neuropathology intergenic_region chr2 106026098 rs34487851 0.00000077 ECRG4 NR NR -0.3 0.740818 ECRG4 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neuritic plaque (NP) Neuropathology intergenic_region chr2 106026098 rs34487851 0.0000025 ECRG4 NR NR NR NA ECRG4 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neuritic plaque (NP)+Cerebral amyloid angiopathy (CAA) Neuropathology intergenic_region chr2 106026098 rs34487851 0.0000045 ECRG4 NR NR -0.25 0.778801 ECRG4 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neurofibrillary tangles (NFT) Neuropathology intergenic_region chr2 106026098 rs34487851 0.0000058 ECRG4 NR NR -0.42 0.657047 ECRG4 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All AD AD intergenic_region chr2 106026098 rs34487851 0.000021 ECRG4 NR NR NR NA ECRG4 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neurofibrillary tangles (NFT)+Cerebral amyloid angiopathy (CAA) Neuropathology intergenic_region chr2 106026098 rs34487851 0.06 ECRG4 NR NR -0.14 0.869358 ECRG4 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Cerebral amyloid angiopathy (CAA) Neuropathology intergenic_region chr2 107062032 rs1357692 0.00000328 NR NR NR NR NA ST6GAL2 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intergenic_region chr2 107062032 rs1357692 0.00000927 NR NR NR 0.86 0.86 ST6GAL2 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intergenic_region chr2 107062032 rs1357692 0.00463 NR NR NR 0.82 0.82 ST6GAL2 SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD intergenic_region chr2 107062032 rs1357692 0.0167 NR NR NR 0.82 0.82 ST6GAL2 SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD intergenic_region chr2 107062032 rs1357692 0.0482 NR NR NR 0.87 0.87 ST6GAL2 SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD intergenic_region chr2 107062032 rs1357692 0.0517 NR NR NR 0.88 0.88 ST6GAL2 SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD intergenic_region chr2 107062032 rs1357692 0.789 NR NR NR 1.05 1.05 ST6GAL2 SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD intergenic_region chr2 112785383 rs1800587 0.44 IL1A A A 0.94 0.94 IL1A SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD upstream_gene_variant chr2 112832813 rs1143634 0.3 IL1B A A 0.91 0.91 IL1B SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD synonymous_variant chr2 118078449 rs7566605 0.111 NR C C 0.93 0.93 INSIG2 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr2 118078449 rs7566605 0.665 NR C C 0.984 0.984 INSIG2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr2 118078449 rs7566605 0.953 NR C C 0 1 INSIG2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr2 119082508 rs893769 0.000000892 NR C C -0.1 0.904837 C1QL2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr2 119087741 rs17189298 0.00000039 NR A A NR NA C1QL2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr2 119087741 rs17189298 0.000000866 NR A A NR NA C1QL2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr2 119110132 rs895401 0.00000089 NR G G NR NA C1QL2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intergenic_region chr2 122368903 rs10496584 0.0000041 NR NR NR 158.69 828307003131138266429592803503575878641942669209922682113970101288960 TSN SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intergenic_region chr2 122368903 rs10496584 0.00034 NR G G 165.94 1166343106910857841078271591364990868937452447467395666572276042085433344 TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122368903 rs10496584 0.00099 NR G G NR NA TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122368903 rs10496584 0.0037 NR G G 149.68 101204086996127604347682722573438191404119470668879906903831871488 TSN SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intergenic_region chr2 122370213 rs2037892 0.00000479 NR NR NR 156.7 113225778192516786193190889471681656767738112808267176411180728057856 TSN SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intergenic_region chr2 122370213 rs2037892 0.00034 NR A A 165.5 751167440329862310341210496192109330500628623044191034523111509259714560 TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122370213 rs2037892 0.00095 NR A A NR NA TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122370213 rs2037892 0.0043 NR A A 145.91 2332963018360591978642695032063321121298145414778130206738612224 TSN SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intergenic_region chr2 122379314 rs1919922 0.00000517 NR NR NR 155.52 34791874300128778888456403724168097534975308740105889483535205531648 TSN SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intergenic_region chr2 122379314 rs1919922 0.00034 NR T T 164.79 369307113359779591940024819131190099933135415107379976682050054086721536 TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122379314 rs1919922 0.0009 NR T T NR NA TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122379314 rs1919922 0.0046 NR T T 144.16 405408183624573310933534702440465522384679108985781662970281984 TSN SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intergenic_region chr2 122383969 rs4848768 0.00000571 NR NR NR 154.6 13865224383620054112084047847760197899086552558971444722899747864576 TSN SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intergenic_region chr2 122383969 rs4848768 0.00035 NR G G 163.94 157847374724851772171017218428284868749599183779615801998914315001790464 TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122383969 rs4848768 0.00087 NR G G NR NA TSN SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intergenic_region chr2 122383969 rs4848768 0.0049 NR G G 143.1 140456020772087941672936762360645236528707767932809320364769280 TSN SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intergenic_region chr2 127038444 rs12476995 0.000475 BIN1 G G 1.25 NA BIN1 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intergenic_region chr2 127082205 rs10194375 0.000000361 BIN1 NR NR NR NA BIN1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr2 127082205 rs10194375 0.0276 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr2 127082205 rs10194375 0.336 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 127082205 rs10194375 0.389 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 127082205 rs10194375 0.659 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr2 127083761 rs13426725 0.0416 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 127083761 rs13426725 0.0715 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr2 127083761 rs13426725 0.085 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr2 127083761 rs13426725 0.329 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr2 127084807 rs11691237 0.0098 BIN1 T T 1.52 1.52 BIN1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr2 127094445 rs10207628 0.00000146 BIN1 NR NR 0.71 0.71 BIN1 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intron_variant chr2 127104557 rs6431219 0.34 BIN1 NR NR 1.04 1.04 BIN1 SNP-based Disease risk 30979435 Caucasian ADGC 6341 Age >=80 y AD AD intron_variant chr2 127104557 rs6431219 6.06E-14 BIN1 NR NR 1.23 1.23 BIN1 SNP-based Disease risk 30979435 Caucasian ADGC 14225 Age 60-79 y AD AD intron_variant chr2 127110859 rs6743470 7.35E-08 "BIN1, CYP27C1" NR NR NR NA BIN1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr2 127115459 rs4663098 0.0285 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr2 127115459 rs4663098 0.368 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr2 127115459 rs4663098 0.646 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr2 127115459 rs4663098 0.714 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr2 127130409 rs12989701 0.00000468 NR A A NR NA BIN1 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intergenic_region chr2 127130409 rs12989701 0.0000895 BIN1 T T 2.16 2.16 BIN1 SNP-based Disease risk 21390209 Caucasian ADNI 496 All AD AD intergenic_region chr2 127130409 rs12989701 0.00112 BIN1 T T 1.17 1.17 BIN1 SNP-based Disease risk 21390209 Caucasian Cohort from Europe Refer to Harold et al(2009) All AD AD intergenic_region chr2 127130409 rs12989701 0.00216 BIN1 T T 1.34 1.34 BIN1 SNP-based Disease risk 21390209 Caucasian Genizon 1502 All AD AD intergenic_region chr2 127130409 rs12989701 0.00372 BIN1 T T 1.34 1.34 BIN1 SNP-based Disease risk 21390209 Caucasian ADGC 1525 All AD AD intergenic_region chr2 127130409 rs12989701 0.0372 BIN1 T T 1.25 1.25 BIN1 SNP-based Disease risk 21390209 Caucasian Cohort from Europe Refer to Harold et al(2009) All AD AD intergenic_region chr2 127130409 rs12989701 0.0526 BIN1 T T 1.2 1.2 BIN1 SNP-based Disease risk 21390209 Caucasian GenADA 1574 All AD AD intergenic_region chr2 127130409 rs12989701 0.482 BIN1 T T 1.08 1.08 BIN1 SNP-based Disease risk 21390209 Caucasian Cohort from USA Refer to Harold et al(2009) All AD AD intergenic_region chr2 127130409 rs12989701 0.497 BIN1 NR NR NR NA BIN1 SNP-based Endophenotype 21390209 Caucasian "ADNI, leadC" 597 AD subjects AD Progression Cognitive intergenic_region chr2 127130409 rs12989701 3.16E-10 BIN1 T T 1.23 1.23 BIN1 SNP-based Disease risk 21390209 Caucasian "ADNI, Cohorts from Europe and USA" 16881 All AD AD intergenic_region chr2 127130545 rs11685593 0.0098 BIN1 T T 1.66 1.66 BIN1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr2 127130545 rs11685593 0.0147 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr2 127130545 rs11685593 0.454 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr2 127130545 rs11685593 0.501 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr2 127130545 rs11685593 0.522 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.000003 BIN1 NR NR 1.16 1.16 BIN1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intergenic_region chr2 127132061 rs7561528 0.0000994 BIN1 NR NR 1.29 1.29 BIN1 SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.000121 BIN1 A A 1.15 1.15 BIN1 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.000137 BIN1 A A 1.15 1.15 BIN1 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.000296 BIN1 NR NR 1.27 1.27 BIN1 SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.0003 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr2 127132061 rs7561528 0.000478 BIN1 A A -0.31 0.733447 BIN1 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intergenic_region chr2 127132061 rs7561528 0.0008 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr2 127132061 rs7561528 0.001 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr2 127132061 rs7561528 0.00107 BIN1 NR NR 1.26 1.26 BIN1 SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.004 BIN1 NR NR -0.121 0.886034 BIN1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Entorhinal cortex thickness Imaging intergenic_region chr2 127132061 rs7561528 0.00536 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr2 127132061 rs7561528 0.009 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.00985 BIN1 A A -0.32 0.726149 BIN1 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intergenic_region chr2 127132061 rs7561528 0.0182 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.02 BIN1 NR NR -0.041 0.959829 BIN1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Temporal pole cortex thickness Imaging intergenic_region chr2 127132061 rs7561528 0.0299 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.03 BIN1 NR NR 1.29 1.29 BIN1 SNP-based Disease risk 20558387 Caucasian ADNI 740 All AD + MCI AD intergenic_region chr2 127132061 rs7561528 0.0377 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.0438 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intergenic_region chr2 127132061 rs7561528 0.06 BIN1 NR NR -0.055 0.946485 BIN1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Hippocampal volume Imaging intergenic_region chr2 127132061 rs7561528 0.0801 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intergenic_region chr2 127132061 rs7561528 0.0866 BIN1 NR NR 1.14 1.14 BIN1 SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.09 BIN1 NR NR -0.02 0.980199 BIN1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Amygdala volume Imaging intergenic_region chr2 127132061 rs7561528 0.0905 BIN1 NR NR 1.34 1.34 BIN1 SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.0959 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intergenic_region chr2 127132061 rs7561528 0.118 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intergenic_region chr2 127132061 rs7561528 0.146 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intergenic_region chr2 127132061 rs7561528 0.17 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intergenic_region chr2 127132061 rs7561528 0.24 BIN1 NR NR -0.019 0.981179 BIN1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Parahippocampal gyrus cortex thickness Imaging intergenic_region chr2 127132061 rs7561528 0.327 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr2 127132061 rs7561528 0.463 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.499 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr2 127132061 rs7561528 0.5 BIN1 NR NR 0.017 1.01715 BIN1 SNP-based Endophenotype 20558387 Caucasian ADNI 740 All White matter lesion volume Imaging intergenic_region chr2 127132061 rs7561528 0.697 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intergenic_region chr2 127132061 rs7561528 0.757 NR A A -0.01 0.99005 BIN1 SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology intergenic_region chr2 127132061 rs7561528 2.86E-11 BIN1 A A 1.18 1.18 BIN1 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intergenic_region chr2 127132061 rs7561528 4.22E-14 BIN1 A A 1.17 1.17 BIN1 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intergenic_region chr2 127132061 rs7561528 4.80E-09 BIN1 NR NR NR NA BIN1 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intergenic_region chr2 127132061 rs7561528 5.21E-14 BIN1 A A 1.17 1.17 BIN1 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intergenic_region chr2 127132061 rs7561528 6.00E-11 BIN1 NR NR 1.25 1.25 BIN1 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intergenic_region chr2 127132061 rs7561528 6.54E-18 BIN1 NR NR NR NA BIN1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr2 127132061 rs7561528 7.66E-11 BIN1 A A 1.18 1.18 BIN1 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intergenic_region chr2 127133851 rs4663105 1.80E-12 BIN1 C C 1.19 1.19 BIN1 SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD intergenic_region chr2 127133851 rs4663105 2.50E-09 BIN1 C C 1.19 1.19 BIN1 SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 21345 APOE-e4+ subjects AD AD intergenic_region chr2 127133851 rs4663105 3.38E-44 BIN1 C C 13.94 NA BIN1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intergenic_region chr2 127133851 rs4663105 3.58E-29 BIN1 C C NR NA BIN1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intergenic_region chr2 127133851 rs4663105 5.46E-26 BIN1 C C NR NA BIN1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intergenic_region chr2 127135234 rs6733839 0.000000151 BIN1 NR NR 0.07 1.07251 BIN1 SNP-based eQTL 30448613 Caucasian ADNI 763 All BIN1 (11719631_s_at) expression in blood Expression intergenic_region chr2 127135234 rs6733839 0.00000205 BIN1 NR NR 0.08 1.08329 BIN1 SNP-based eQTL 30448613 Caucasian ADNI 763 All BIN1 (11746895_a_at) expression in blood Expression intergenic_region chr2 127135234 rs6733839 0.0000034 BIN1 T T 1.39 1.39 BIN1 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intergenic_region chr2 127135234 rs6733839 0.00025 BIN1 T T 1.36 1.36 BIN1 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intergenic_region chr2 127135234 rs6733839 0.000894 BIN1 T T NR NA BIN1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intergenic_region chr2 127135234 rs6733839 0.00805 BIN1 T T 1.17 1.17 BIN1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr2 127135234 rs6733839 1.44E-45 BIN1 T T 1.21 1.21 BIN1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr2 127135234 rs6733839 1.70E-26 BIN1 T T 1.21 1.21 BIN1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intergenic_region chr2 127135234 rs6733839 2.00E-18 BIN1 T T 1.23 1.23 BIN1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intergenic_region chr2 127135234 rs6733839 2.10E-44 BIN1 T T 1.2 1.2 BIN1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intergenic_region chr2 127135234 rs6733839 3.16E-11 BIN1 NR NR -0.15 NA BIN1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intergenic_region chr2 127135234 rs6733839 3.40E-19 BIN1 T T 1.24 1.24 BIN1 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intergenic_region chr2 127135234 rs6733839 4.00E-28 BIN1 T T 1.18 1.18 BIN1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intergenic_region chr2 127135234 rs6733839 6.90E-44 BIN1 T T 1.22 1.22 BIN1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intergenic_region chr2 127135234 rs6733839 6.94E-44 BIN1 T T 1.22 1.22 BIN1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr2 127135234 rs6733839 7.11E-26 BIN1 T T NR NA BIN1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr2 127135234 rs6733839 NR BIN1 T T 0.96 0.96 BIN1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intergenic_region chr2 127135234 rs6733839 NR ZCWPW1 T T 1.02 1.02 BIN1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intergenic_region chr2 127135234 rs6733839 NR ZCWPW1 T T 1.06 1.06 BIN1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intergenic_region chr2 127137039 rs744373 0.00000102 BIN1 G G 1.14 1.14 BIN1 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intergenic_region chr2 127137039 rs744373 0.0000032 BIN1 NR NR 1.17 1.17 BIN1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intergenic_region chr2 127137039 rs744373 0.000038 BIN1 NR NR 1.17 1.17 BIN1 SNP-based Disease risk 21460840 Caucasian GERAD 9799 All AD AD intergenic_region chr2 127137039 rs744373 0.0000492 BIN1 G G 1.37 1.37 BIN1 SNP-based Disease risk 21390209 Caucasian GenADA 1574 All AD AD intergenic_region chr2 127137039 rs744373 0.000139 BIN1 G G 1.25 1.25 BIN1 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intergenic_region chr2 127137039 rs744373 0.000184 BIN1 G G 1.16 1.16 BIN1 SNP-based Disease risk 21390209 Caucasian Cohort from Europe Refer to Harold et al(2009) All AD AD intergenic_region chr2 127137039 rs744373 0.000493 BIN1 G G 1.13 1.13 BIN1 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intergenic_region chr2 127137039 rs744373 0.0007 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr2 127137039 rs744373 0.0007 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr2 127137039 rs744373 0.0007 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intergenic_region chr2 127137039 rs744373 0.00145 BIN1 G G 1.31 1.31 BIN1 SNP-based Disease risk 21390209 Caucasian Cohort from Europe Refer to Harold et al(2009) All AD AD intergenic_region chr2 127137039 rs744373 0.02 BIN1 NR NR 1.17 1.17 BIN1 SNP-based Disease risk 20460622 Caucasian Cohort from Europe 2349 All AD AD intergenic_region chr2 127137039 rs744373 0.0237 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intergenic_region chr2 127137039 rs744373 0.0383 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intergenic_region chr2 127137039 rs744373 0.04 BIN1 NR NR 1.2 1.2 BIN1 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intergenic_region chr2 127137039 rs744373 0.0565 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr2 127137039 rs744373 0.0604 BIN1 G G 1.16 1.16 BIN1 SNP-based Disease risk 21390209 Caucasian Genizon 1502 All AD AD intergenic_region chr2 127137039 rs744373 0.0671 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intergenic_region chr2 127137039 rs744373 0.0687 BIN1 G G 1.16 1.16 BIN1 SNP-based Disease risk 21390209 Caucasian ADGC 1525 All AD AD intergenic_region chr2 127137039 rs744373 0.0894 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intergenic_region chr2 127137039 rs744373 0.128 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intergenic_region chr2 127137039 rs744373 0.187 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intergenic_region chr2 127137039 rs744373 0.22 BIN1 NR NR NR NA BIN1 SNP-based Endophenotype 21390209 Caucasian "ADNI, leadC" 597 AD subjects AD Progression Cognitive intergenic_region chr2 127137039 rs744373 0.227 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intergenic_region chr2 127137039 rs744373 0.272 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intergenic_region chr2 127137039 rs744373 0.405 BIN1 G G 1.07 1.07 BIN1 SNP-based Disease risk 21390209 Caucasian Cohort from USA Refer to Harold et al(2009) All AD AD intergenic_region chr2 127137039 rs744373 0.515 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intergenic_region chr2 127137039 rs744373 0.805 BIN1 G G 0.98 0.98 BIN1 SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intergenic_region chr2 127137039 rs744373 0.973 CUGBP2 NR NR NR NA BIN1 SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intergenic_region chr2 127137039 rs744373 0.999 BIN1 G G 1 1 BIN1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr2 127137039 rs744373 1.32E-10 BIN1 G G 1.19 1.19 BIN1 SNP-based Disease risk 21390209 Caucasian "ADNI, Cohorts from Europe and USA" 16881 All AD AD intergenic_region chr2 127137039 rs744373 1.50E-10 BIN1 NR NR 1.17 1.17 BIN1 SNP-based Disease risk 21460840 Caucasian "ADC, EADI, GERAD" 20373 All AD AD intergenic_region chr2 127137039 rs744373 1.59E-11 BIN1 G G 1.15 1.15 BIN1 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intergenic_region chr2 127137039 rs744373 2.60E-14 BIN1 NR NR 1.17 1.17 BIN1 SNP-based Disease risk 21460840 Caucasian "ADGC, CHARGE, EADI, GERAD" 59716 All AD AD intergenic_region chr2 127204917 rs7585314 0.003 BIN1 T T 0.75 0.75 CYP27C1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr2 127284258 rs4150436 0.00403 ERCC3 C C NR NA ERCC3 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr2 127284258 rs4150436 1.72E-21 NR C C NR NA ERCC3 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group ERCC3 (ILMN_1740216) expresssion Expression intron_variant chr2 131824938 rs12470837 0.00000116 LOC647996 NR NR 0.336 1.39934 CCDC74A SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker downstream_gene_variant chr2 131824938 rs12470837 0.00000137 LOC647996 NR NR 0.468 1.5968 CCDC74A SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker downstream_gene_variant chr2 131824938 rs12470837 0.00000137 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131824938 rs12470837 0.0122 LOC647996 NR NR 0.243 1.27507 CCDC74A SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker downstream_gene_variant chr2 131825705 rs10928155 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131827077 rs9711604 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131827540 rs12469076 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131828237 rs6709732 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131828417 rs6709893 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131828659 rs6740860 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131829097 rs2314388 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131829281 rs4558626 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr2 131831662 rs12473669 0.0000022 MGC50273 NR NR NR NA CCDC74A SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr2 133575190 rs7588354 0.00000137 NCKAP5 A A 0.66 NA NCKAP5 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intergenic_region chr2 142202362 rs2890652 0.421 NR C C 0.963 0.963 LRP1B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr2 142202362 rs2890652 0.85 NR C C 1.01 1.01 LRP1B SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr2 142202362 rs2890652 0.876 NR C C 0.001 1.001 LRP1B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr2 142202362 rs2890652 0.994 NR C C 1 1 LRP1B SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr2 148800291 rs2121433 <1.00E-06 EPC2 NR NR NR NA EPC2 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau Fluid biomarker intergenic_region chr2 148801056 rs1374441 <1.00E-06 EPC2 NR NR NR NA EPC2 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau Fluid biomarker intergenic_region chr2 148810827 rs4499362 <1.00E-06 EPC2 NR NR NR NA EPC2 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau Fluid biomarker intergenic_region chr2 148810827 rs4499362 <1.00E-06 EPC2 NR NR NR NA EPC2 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau/Ab1-42 Fluid biomarker intergenic_region chr2 148811160 rs10171238 <1.00E-06 EPC2 NR NR NR NA EPC2 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau Fluid biomarker intergenic_region chr2 148811160 rs10171238 <1.00E-06 EPC2 NR NR NR NA EPC2 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF T-tau/Ab1-42 Fluid biomarker intergenic_region chr2 153374900 rs13397414 0.00028 NR G G NR NA RPRM SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD downstream_gene_variant chr2 153374900 rs13397414 0.0003 NR G G NR NA RPRM SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD downstream_gene_variant chr2 153374900 rs13397414 3.44E-09 Intergenic (as reported in paper) G G NR NA RPRM SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD downstream_gene_variant chr2 158121282 rs2074955 0.000000109 UPP2 C C NR NA UPP2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF P-tau181p Fluid biomarker intron_variant chr2 158121282 rs2074955 0.000000207 UPP2 C C NR NA UPP2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF P-tau181p Fluid biomarker intron_variant chr2 160224330 rs12692585 0.000021 "ITGB6, RBMS1" NR NR NR NA ITGB6 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr2 160489936 rs7569522 0.000025 RBMS1 NR NR NR NA RBMS1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr2 162782597 rs1032412 0.00019 KCNH7 G G NR NA KCNH7 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr2 162782597 rs1032412 0.0024 KCNH7 G G NR NA KCNH7 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr2 162782597 rs1032412 0.0097 KCNH7 G G NR NA KCNH7 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr2 165270773 rs2119067 0.0000438 NR NR NR NR NA SCN2A SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr2 165271418 rs10184275 0.000022 NR NR NR NR NA SCN2A SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr2 168286525 rs9917256 0.79 STK39 A A NR NA STK39 SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intergenic_region chr2 168286525 rs9917256 1.62E-09 STK39 A A NR NA STK39 SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intergenic_region chr2 169780132 rs11894266 0.00000069 SSB NR NR 0.86 0.86 KLHL23 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD downstream_gene_variant chr2 172040778 rs34737109 0.23 NR A A -0.08 0.923116 METAP1D SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr2 184913701 rs1344706 0.54 ZNF804A NR NR 0.95 0.95 ZNF804A SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr2 184913701 rs1344706 0.79 ZNF804A NR NR 0.99 0.99 ZNF804A SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr2 192871656 rs1373900 0.0000538 Intergenic (as reported in paper) T T NR NA TMEFF2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr2 192871656 rs1373900 0.00037 NR T T NR NA TMEFF2 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr2 192871656 rs1373900 0.0087 NR T T NR NA TMEFF2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr2 201399433 rs13022344 0.001 TRAK2 NR NR 1.07 1.07 TRAK2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD missense_variant chr2 201399433 rs13022344 0.0051 TRAK2 NR NR NR NA TRAK2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD missense_variant chr2 201399433 rs13022344 0.0077 TRAK2 NR NR NR NA TRAK2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD missense_variant chr2 201399433 rs13022344 0.015 TRAK2 NR NR NR NA TRAK2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD missense_variant chr2 201399433 rs13022344 0.628 TRAK2 NR NR NR NA TRAK2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD missense_variant chr2 201399433 rs13022344 0.821 TRAK2 NR NR NR NA TRAK2 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD missense_variant chr2 204481944 rs12613305 0.00000936 PARD3B A A 0.13 1.13883 PARD3B SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intron_variant chr2 207489233 rs80140096 0.009 CREB1 G G 0.08 1.08329 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207489233 rs80140096 0.034 CREB1 G G 0.05 1.05127 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr2 207489233 rs80140096 0.77 CREB1 G G -0.02 0.980199 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207489233 rs80140096 0.904 CREB1 G G 0 1 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr2 207490606 rs72954151 0.008 CREB1 G G 0.07 1.07251 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207490606 rs72954151 0.066 CREB1 G G 0.04 1.04081 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr2 207490606 rs72954151 0.439 CREB1 G G -0.04 0.960789 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207490606 rs72954151 0.671 CREB1 G G 0.01 1.01005 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr2 207498338 rs2042484 0.046 CREB1 T T 0.08 1.08329 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207498338 rs2042484 0.286 CREB1 T T -0.02 0.980199 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207498338 rs2042484 0.829 CREB1 T T 0 1 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr2 207498338 rs2042484 0.856 CREB1 T T 0 1 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr2 207527491 rs74844716 0.04 CREB1 T T 0.09 1.09417 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207527491 rs74844716 0.106 CREB1 T T 0.06 1.06184 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr2 207527491 rs74844716 0.188 CREB1 T T 0.04 1.04081 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr2 207527491 rs74844716 0.756 CREB1 T T -0.03 0.970446 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207578862 rs55834243 0.046 CREB1 C C 0.11 1.11628 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with non-APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207578862 rs55834243 0.155 CREB1 C C 0.09 1.09417 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 11840 Demented subjects Episodic Memory Performance Cognitive intron_variant chr2 207578862 rs55834243 0.256 CREB1 C C -0.1 0.904837 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly with APOE-e4 carriers Episodic Memory Performance Cognitive intron_variant chr2 207578862 rs55834243 0.302 CREB1 C C 0.05 1.05127 CREB1 SNP-based Endophenotype 25150575 Caucasian ADGC 2764 Cognitively healthy elderly Episodic Memory Performance Cognitive intron_variant chr2 215750203 rs6758001 0.00000887 LINC00607 NR NR 0.64 1.89648 MREG SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr2 215750203 rs6758001 0.0000778 LINC00607 NR NR 0.77 2.15977 MREG SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr2 215750203 rs6758001 0.0171 LINC00607 NR NR 0.51 1.66529 MREG SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr2 226697423 rs7558386 0.000000108 NR G G NR NA IRS1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF P-tau181p Fluid biomarker intergenic_region chr2 226697423 rs7558386 0.000000527 NR G G 0.24 1.27125 IRS1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF P-tau181p Fluid biomarker intergenic_region chr2 227199464 rs10498214 0.0812 COL4A3 NR NR NR NA COL4A3 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr2 227356053 rs7560053 1.40E-67 MFF NR NR 0.3 1.34986 MFF SNP-based eQTL 22685416 Caucasian MAYO 399 All MFF expression in Temporal cortex Expression intron_variant chr2 231201938 rs753855 0.00000409 "ARMC9, HTR2B, PSMD1" NR NR NR NA ARMC9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr2 231201938 rs753855 0.00000982 "ARMC9, HTR2B, PSMD1" NR NR NR NA ARMC9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr2 231201938 rs753855 0.0007 "ARMC9, HTR2B, PSMD1" NR NR 0.91 2.48432 ARMC9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intron_variant chr2 231201938 rs753855 0.00475 "ARMC9, HTR2B, PSMD1" NR NR 0.69 1.99372 ARMC9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intron_variant chr2 231201938 rs753855 0.536 "ARMC9, HTR2B, PSMD1" NR NR 1.13 3.09566 ARMC9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intron_variant chr2 233117202 rs10933431 0.00000026 INPP5D G G 0.9 0.9 INPP5D SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr2 233117202 rs10933431 0.00000167 INPPD5 G G NR NA INPP5D SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr2 233117202 rs10933431 0.00000251 INPPD5 G G NR NA INPP5D SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr2 233117202 rs10933431 0.0032 INPP5D G G 0.92 0.92 INPP5D SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr2 233117202 rs10933431 3.40E-09 INPP5D G G 0.91 0.91 INPP5D SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr2 233117202 rs10933431 8.92E-10 INPPD5 G G -6.13 NA INPP5D SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr2 233117495 rs7421448 0.0000152 INPP5D T T 0.99 0.99 INPP5D SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr2 233117495 rs7421448 0.000223 INPP5D T T 0.91 0.91 INPP5D SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr2 233117495 rs7421448 0.000559 INPP5D T T 0.92 0.92 INPP5D SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr2 233117495 rs7421448 0.000584 INPP5D T T NR NA INPP5D SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr2 233117495 rs7421448 0.00145 INPP5D T T NR NA INPP5D SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr2 233117495 rs7421448 0.575 INPP5D T T 1.06 1.06 INPP5D SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr2 233138407 rs10202748 0.0079 INPP5D NR NR -0.06 NA INPP5D SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr2 233159830 rs35349669 0.000000032 INPP5D T T 1.08 1.08 INPP5D SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr2 233159830 rs35349669 0.000057 INPP5D T T 1.1 1.1 INPP5D SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr2 233159830 rs35349669 0.000096 INPP5D T T 1.07 1.07 INPP5D SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr2 233159830 rs35349669 0.0231 INPP5D T T 1.104 1.104 INPP5D SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr2 233159830 rs35349669 0.21 INPP5D NR NR 0.89 0.89 INPP5D SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr2 233159830 rs35349669 0.84 DSG2 T T 0.98 0.98 INPP5D SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr2 233159830 rs35349669 0.84 INPP5D T T 1.01 1.01 INPP5D SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr2 233159830 rs35349669 NR INPP5D T T 0.88 0.88 INPP5D SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr2 233159830 rs35349669 NR ZCWPW1 T T 0.75 0.75 INPP5D SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr2 233159830 rs35349669 NR ZCWPW1 T T 1.07 1.07 INPP5D SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr2 233206691 rs3792117 0.000453 INPP5D A A 1.55 NA INPP5D SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr2 239166779 rs3791523 0.455 HDAC4 NR NR NR NA HDAC4 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr2 240285947 rs4417745 0.0000252 OTOS A A 1.36 1.36 OTOS SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intergenic_region chr2 240285947 rs4417745 0.00032 OTOS A A 1.22 1.22 OTOS SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intergenic_region chr2 240285947 rs4417745 0.47 OTOS A A 1.06 1.06 OTOS SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intergenic_region chr20 1154256 rs2300186 0.0000393 PSMF1 NR NR 0.41 0.41 PSMF1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr20 1154769 rs2300185 0.0000451 PSMF1 NR NR 0.42 0.42 PSMF1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr20 1155512 rs6074191 0.0000431 PSMF1 NR NR 0.41 0.41 PSMF1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr20 1156012 rs4813945 0.0000451 PSMF1 NR NR 0.42 0.42 PSMF1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr20 1156560 rs6134051 0.0000455 PSMF1 NR NR 0.43 0.43 PSMF1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr20 1165492 rs2072965 0.0000364 PSMF1 NR NR 0.41 0.41 PSMF1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD 3_prime_UTR_variant chr20 1168139 rs4813044 0.0000397 PSMF1 NR NR 0.44 0.44 PSMF1 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD 3_prime_UTR_variant chr20 1723468 rs6135782 0.00000618 NR NR NR NR NA SIRPG SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.000158 NR NR NR 0.5 0.5 SIRPG SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.00163 NR NR NR NR NA SIRPG SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.00219 NR NR NR NR NA SIRPG SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.0335 NR NR NR 0.56 0.56 SIRPG SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.0498 NR NR NR 0.42 0.42 SIRPG SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.15025 NR NR NR NR NA SIRPG SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.61181 NR NR NR NR NA SIRPG SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD upstream_gene_variant chr20 1723468 rs6135782 0.709 NR NR NR NR NA SIRPG SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD upstream_gene_variant chr20 4696446 rs6107516 0.009 PRNP A A 0.73 0.73 PRNP SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1374 All AD AD intron_variant chr20 4696446 rs6107516 0.19 PRNP A A 0.68 0.68 PRNP SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1374 All Age of AD onset Other intron_variant chr20 23637790 rs1064039 0.033 CST3 T T 0.83 0.83 CST3 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD missense_variant chr20 23656343 rs2424590 0.00000475 CST3 NR NR -0.04 0.960789 CST3 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma Cystatin-C Fluid biomarker non_coding_transcript_exon_variant chr20 25618924 rs2387976 1.72E-32 NANP NR NR -0.57 0.565525 NANP SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD NANP expression in Cerebellar Expression intron_variant chr20 25618924 rs2387976 4.25E-73 NANP NR NR -0.54 0.582748 NANP SNP-based eQTL 22685416 Caucasian MAYO 374 All NANP expression in Cerebellar Expression intron_variant chr20 25618924 rs2387976 5.29E-84 NANP NR NR -0.65 0.522046 NANP SNP-based eQTL 22685416 Caucasian MAYO 399 All NANP expression in Temporal cortex Expression intron_variant chr20 25618924 rs2387976 6.29E-35 NANP NR NR -0.51 0.600496 NANP SNP-based eQTL 22685416 Caucasian MAYO 197 AD NANP expression in Cerebellar Expression intron_variant chr20 31422680 rs6059244 0.0000476 NR NR NR NR NA DEFB121 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr20 31431051 rs2180566 0.000038 DEFB123 NR NR NR NA DEFB123 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD upstream_gene_variant chr20 35038413 rs6087664 5.63E-11 NR NR NR NR NA TRPC4AP SNP-based Disease risk 18449908 Caucasian Cohort from USA 70 All AD AD intron_variant chr20 35050785 rs6088692 5.63E-11 NR NR NR NR NA TRPC4AP SNP-based Disease risk 18449908 Caucasian Cohort from USA 70 All AD AD intron_variant chr20 35056555 rs6120816 6.99E-11 NR NR NR NR NA TRPC4AP SNP-based Disease risk 18449908 Caucasian Cohort from USA 70 All AD AD intron_variant chr20 35057846 rs1885119 5.63E-11 NR NR NR NR NA TRPC4AP SNP-based Disease risk 18449908 Caucasian Cohort from USA 70 All AD AD intron_variant chr20 35119019 rs2065108 3.85E-10 NR NR NR NR NA EDEM2 SNP-based Disease risk 18449908 Caucasian Cohort from USA 70 All AD AD intron_variant chr20 35125836 rs6088727 3.85E-10 NR NR NR NR NA EDEM2 SNP-based Disease risk 18449908 Caucasian Cohort from USA 70 All AD AD intron_variant chr20 35335763 rs2425062 0.000201 UQCC G G NR NA UQCC1 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr20 35335763 rs2425062 4.58E-13 NR G G NR NA UQCC1 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) UQCC (ILMN_1724734) expression in peripheral blood Expression intron_variant chr20 36232134 rs41293100 0.00309 AAR2 A A NR NA EPB41L1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD 3_prime_UTR_variant chr20 36232134 rs41293100 1.31E-35 NR A A NR NA EPB41L1 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AAR2 (ILMN_1721225) expression Expression 3_prime_UTR_variant chr20 36483848 rs118164920 0.00588 NDRG3 G G NR NA DLGAP4 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD intron_variant chr20 36483848 rs118164920 3.15E-51 NR G G NR NA DLGAP4 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group NDRG3 (ILMN_1738229) expression Expression intron_variant chr20 37771178 rs6013029 0.389 NR T T 0.93 0.93 CTNNBL1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr20 37771178 rs6013029 0.4 NR T T 1.094 1.094 CTNNBL1 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr20 37771178 rs6013029 0.533 NR T T 0.969 0.969 CTNNBL1 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr20 37771178 rs6013029 0.706 NR T T 0 1 CTNNBL1 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr20 46113425 rs1569723 9.61E-14 CD40 NR NR -0.06 0.941765 CD40 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma CD40 Fluid biomarker upstream_gene_variant chr20 46148656 rs6032678 0.00238 CD40 NR NR 0.09 1.09417 CD40 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma CD40 Fluid biomarker intergenic_region chr20 56402450 rs2426622 0.00461 CASS4 G G 0.83 NA CSTF1 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr20 56422512 rs6024870 0.000000035 CASS4 A A 0.88 0.88 CASS4 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr20 56422512 rs6024870 0.0000011 CASS4 A A 0.88 0.88 CASS4 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr20 56422512 rs6024870 0.009 CASS4 A A 0.9 0.9 CASS4 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr20 56423488 rs6014724 0.00000632 CASS4 G G NR NA CASS4 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr20 56423488 rs6014724 6.56E-10 CASS4 G G -6.18 NA CASS4 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr20 56423488 rs6014724 8.72E-08 CASS4 G G NR NA CASS4 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr20 56443204 rs7274581 0.000000025 CASS4 C C 0.88 0.88 CASS4 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr20 56443204 rs7274581 0.0000016 CASS4 C C 0.87 0.87 CASS4 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr20 56443204 rs7274581 0.0033 CASS4 C C 0.73 0.73 CASS4 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr20 56443204 rs7274581 0.0041 CASS4 C C 0.89 0.89 CASS4 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr20 56443204 rs7274581 0.0079 CASS4 NR NR 0.1 NA CASS4 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr20 56443204 rs7274581 0.011 CASS4 C C 0.72 0.72 CASS4 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr20 56443204 rs7274581 0.52 CASS4 NR NR 1.12 1.12 CASS4 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr20 56443204 rs7274581 0.815 CASS4 C C 1.017 1.017 CASS4 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr20 56443204 rs7274581 NR CASS4 T T 1.12 1.12 CASS4 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr20 56443204 rs7274581 NR ZCWPW1 T T 1.03 1.03 CASS4 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr20 56443204 rs7274581 NR ZCWPW1 T T 1.53 1.53 CASS4 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr20 57563565 rs8192708 0.000099 PCK1 NR NR 1.29 1.29 PCK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD missense_variant&splice_region_variant chr20 57563565 rs8192708 0.0033 PCK1 NR NR NR NA PCK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD missense_variant&splice_region_variant chr20 57563565 rs8192708 0.026 PCK1 NR NR NR NA PCK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD missense_variant&splice_region_variant chr20 57563565 rs8192708 0.051 PCK1 NR NR NR NA PCK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD missense_variant&splice_region_variant chr20 57563565 rs8192708 0.396 PCK1 NR NR NR NA PCK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD missense_variant&splice_region_variant chr20 57563565 rs8192708 0.791 PCK1 NR NR NR NA PCK1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD missense_variant&splice_region_variant chr20 60323151 rs6027511 0.00000896 NR NR NR -122.24 8.16286e-54 CDH26 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr20 60323151 rs6027511 0.00076 NR C C -121.95 1.09091e-53 CDH26 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr20 60323151 rs6027511 0.00089 NR C C NR NA CDH26 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr20 60323151 rs6027511 0.0038 NR C C -122.62 5.58227e-54 CDH26 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr20 61371988 rs4925189 0.000000635 CDH4 G G 0.2 1.2214 CDH4 SNP-based Endophenotype 20932310 Caucasian ADNI 172 AD CSF T-tau Fluid biomarker intron_variant chr21 14356476 rs2403771 0.0000062 NR NR NR NR NA HSPA13 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr21 14356476 rs2403771 0.00012 NR NR NR NR NA HSPA13 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr21 14356476 rs2403771 0.000158 NR NR NR 0.54 0.54 HSPA13 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr21 14356476 rs2403771 0.00267 NR NR NR 0.53 0.53 HSPA13 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr21 14356476 rs2403771 0.0367 NR NR NR NR NA HSPA13 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr21 14356476 rs2403771 0.126 NR NR NR NR NA HSPA13 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr21 14356476 rs2403771 0.47516 NR NR NR NR NA HSPA13 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr21 14356476 rs2403771 0.51869 NR NR NR NR NA HSPA13 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr21 14356476 rs2403771 0.534 NR NR NR 0.6 0.6 HSPA13 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr21 19368235 rs2825544 0.000000485 PRSS7 C C 1.14 1.14 TMPRSS15 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intergenic_region chr21 19368235 rs2825544 0.000021 PRSS7 C C 1.09 1.09 TMPRSS15 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intergenic_region chr21 19368235 rs2825544 0.000255 PRSS7 C C 1.13 1.13 TMPRSS15 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intergenic_region chr21 20983528 rs1022442 0.000000275 NCAM2 A A NR NA NCAM2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr21 25277446 rs76252969 0.00000486 LINC00158 G G 0.59 0.59 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intron_variant chr21 25517756 rs12386284 0.00000455 MIR155HG T T 1.37 1.37 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr21 25547104 rs1783012 0.00000459 MIR155HG T T 0.73 0.73 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intergenic_region chr21 25547257 rs1783013 0.00000465 MIR155HG T T 0.73 0.73 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intergenic_region chr21 25547744 rs926963 0.00000475 MIR155HG T T 0.73 0.73 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intergenic_region chr21 25568503 rs1893650 0.00000394 MIR155HG T T 1.32 1.32 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr21 25569648 rs2226326 0.00000438 MIR155HG A A 1.32 1.32 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr21 25575998 rs2829803 0.00000409 MIR155HG G G 1.32 1.32 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD downstream_gene_variant chr21 25583969 rs2298369 0.000000311 LINC00515 C C 0.75 0.75 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD upstream_gene_variant chr21 25583969 rs2298369 0.000000367 "LINC00515, MRPL39" C C 0.8 0.8 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD upstream_gene_variant chr21 25599076 rs2829823 0.00000406 MRPL39 A A 1.32 1.32 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr21 25601939 rs2829832 0.00000468 MRPL39 T T 1.32 1.32 MRPL39 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr21 25725147 rs11909995 0.00000441 ATP5J G G 0.62 0.62 ATP5PF SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr21 25731303 rs2829887 0.00000333 "APP, ATP5J" T T -0.14 0.869358 ATP5PF SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intron_variant chr21 26101558 rs2154481 0.000618 APP NR NR 0.95 0.95 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26128343 rs2830072 0.02 APP NR NR 0.96 0.96 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26128825 rs2830073 0.00247 APP NR NR 0.95 0.95 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26130406 rs2830077 0.00276 APP NR NR 0.95 0.95 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26135742 rs432766 0.047 APP NR NR 0.97 0.97 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26142055 rs375369 0.015 APP NR NR 0.96 0.96 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26144759 rs467021 0.00306 APP NR NR 0.95 0.95 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26150590 rs12483003 0.00353 APP NR NR 0.95 0.95 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26158949 rs368196 0.00215 APP NR NR 0.95 0.95 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26160704 rs465235 0.00127 APP NR NR 0.95 0.95 APP SNP-based Disease risk 28671113 Caucasian IGAP 54162 All AD AD intron_variant chr21 26784537 rs2830500 0.000000026 ADAMTS1 A A 0.93 0.93 ADAMTS1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD intergenic_region chr21 26784537 rs2830500 0.000000074 ADAMTS1 A A 0.93 0.93 ADAMTS1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intergenic_region chr21 26784537 rs2830500 0.13 ADAMTS1 A A 0.95 0.95 ADAMTS1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD intergenic_region chr21 27324157 rs239713 0.000000496 NR T T NR NA ADAMTS5 SNP-based Endophenotype 20932310 Caucasian ADNI 172 AD CSF Ab1-42 Fluid biomarker intergenic_region chr21 27903308 rs9305339 0.00000787 LINC00314 NR NR 0.26 1.29693 ADAMTS5 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intergenic_region chr21 27903308 rs9305339 0.000922 LINC00314 NR NR 0.3 1.34986 ADAMTS5 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intergenic_region chr21 27903308 rs9305339 0.00176 LINC00314 NR NR 0.25 1.28403 ADAMTS5 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intergenic_region chr21 31876391 rs2833546 0.11 HUNK NR NR NR NA HUNK SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr21 39209604 rs6517526 1.33E-24 BRWD1 NR NR -0.71 0.491644 BRWD1 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD BRWD1 expression in Cerebellar Expression intron_variant chr21 39209604 rs6517526 2.71E-31 BRWD1 NR NR -0.88 0.414783 BRWD1 SNP-based eQTL 22685416 Caucasian MAYO 197 AD BRWD1 expression in Cerebellar Expression intron_variant chr21 39209604 rs6517526 2.80E-61 BRWD1 NR NR -0.8 0.449329 BRWD1 SNP-based eQTL 22685416 Caucasian MAYO 374 All BRWD1 expression in Cerebellar Expression intron_variant chr21 40135768 rs11700591 0.000000099 NR C C 0.72 2.05443 DSCAM SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr21 40135768 rs11700591 0.00023 NR C C -0.35 0.704688 DSCAM SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr21 40135768 rs11700591 0.89 NR C C -0.02 0.980199 DSCAM SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr21 42257956 rs142544282 0.000000008 NR T T -2.11 0.121238 ABCG1 SNP-based Endophenotype 25188341 Caucasian ADGC 4046 All Neuritic Plaque Neuropathology intron_variant chr21 42679905 rs3819902 0.0004 PDE9A C C NR NA PDE9A SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr21 42679905 rs3819902 0.00068 PDE9A C C NR NA PDE9A SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr21 42679905 rs3819902 0.0009 PDE9A C C NR NA PDE9A SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr21 45264602 rs2838859 1.11E-111 POFUT2 NR NR -0.84 0.431711 POFUT2 SNP-based eQTL 22685416 Caucasian MAYO 399 All POFUT2 expression in Temporal cortex Expression 3_prime_UTR_variant chr21 45264602 rs2838859 1.27E-97 POFUT2 NR NR -0.86 0.423162 POFUT2 SNP-based eQTL 22685416 Caucasian MAYO 374 All POFUT2 expression in Cerebellar Expression 3_prime_UTR_variant chr21 45264602 rs2838859 5.20E-48 POFUT2 NR NR -0.89 0.410656 POFUT2 SNP-based eQTL 22685416 Caucasian MAYO 197 AD POFUT2 expression in Cerebellar Expression 3_prime_UTR_variant chr21 45264602 rs2838859 5.28E-43 POFUT2 NR NR -0.81 0.444858 POFUT2 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD POFUT2 expression in Cerebellar Expression 3_prime_UTR_variant chr22 21619030 rs4821116 0.000402 UBE2L3 T T NR NA UBE2L3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr22 21619030 rs4821116 0.00071 UBE2L3 T T NR NA UBE2L3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr22 21619030 rs4821116 0.11 UBE2L3 T T 1 1 UBE2L3 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr22 21628603 rs2298428 0.00009 YDJC T T NR NA YDJC SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD missense_variant chr22 21628603 rs2298428 0.000105 YDJC C C NR NA YDJC SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD missense_variant chr22 21628603 rs2298428 0.000504 YDJC T T 0.94 0.94 YDJC SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD missense_variant chr22 21628603 rs2298428 0.00134 YDJC T T 0.95 0.95 YDJC SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD missense_variant chr22 21628603 rs2298428 0.19 YDJC T T 1 1 YDJC SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD missense_variant chr22 21628603 rs2298428 0.647 YDJC T T 1.03 1.03 YDJC SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD missense_variant chr22 21628603 rs2298428 1.58E-08 YDJC T T NR NA YDJC SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD missense_variant chr22 21628603 rs2298428 3.38E-10 YDJC C C NR NA YDJC SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 51109 All Crohn disease Non-ADRD missense_variant chr22 27755837 rs2267106 0.0000414 MN1 NR NR NR NA MN1 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr22 30030080 rs41174 0.000834 MTMR3 T T NR NA MTMR3 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD 3_prime_UTR_variant chr22 30030080 rs41174 3.03E-76 NR T T NR NA MTMR3 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) MTMR3 (ILMN_1803925) expression Expression 3_prime_UTR_variant chr22 30361306 rs737950 1.23E-24 SF3A1 NR NR 0.42 1.52196 CCDC157 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD SF3A1 expression in Cerebellar Expression intron_variant chr22 30361306 rs737950 1.68E-28 SF3A1 NR NR 0.45 1.56831 CCDC157 SNP-based eQTL 22685416 Caucasian MAYO 197 AD SF3A1 expression in Cerebellar Expression intron_variant chr22 30361306 rs737950 2.71E-68 SF3A1 NR NR 0.46 1.58407 CCDC157 SNP-based eQTL 22685416 Caucasian MAYO 399 All SF3A1 expression in Temporal cortex Expression intron_variant chr22 30361306 rs737950 9.11E-61 SF3A1 NR NR 0.44 1.55271 CCDC157 SNP-based eQTL 22685416 Caucasian MAYO 374 All SF3A1 expression in Cerebellar Expression intron_variant chr22 32349929 rs5998432 0.00000087 NR T T NR NA RFPL3 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF T-tau Fluid biomarker upstream_gene_variant chr22 39133424 rs11089928 0.00242 APOBEC3F A A NR NA CBX7 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD 3_prime_UTR_variant chr22 39133424 rs11089928 7.21E-20 NR A A NR NA CBX7 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) APOBEC3F (ILMN_2296950) expression Expression 3_prime_UTR_variant chr22 40820742 rs6002167 0.0000227 ST13 NR NR 0.67 0.67 SLC25A17 SNP-based Disease risk 30979435 Caucasian ADGC 6543 Age >=80 y AD AD upstream_gene_variant chr22 40820742 rs6002167 0.502 ST13 NR NR 1.04 1.04 SLC25A17 SNP-based Disease risk 30979435 Caucasian ADGC 14844 Age 60-79 y AD AD upstream_gene_variant chr22 41205381 rs3804097 0.016 L3MBTL2 NR NR 2.99 2.99 L3MBTL2 SNP-based Cross phenotype 30010129 Asian Cohort from Han Chinse 475 All AD AD missense_variant chr22 41217299 rs9611520 0.00014 L3MBTL2 NR NR NR NA L3MBTL2 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr22 41217299 rs9611520 0.0096 NA NR NR NR NA L3MBTL2 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr22 41822852 rs7364180 <1.00E-06 EPC2 NR NR NR NA CCDC134 SNP-based Endophenotype 21123754 Non-Hispanic Caucasian ADNI 374 All CSF Ab1-42 Fluid biomarker intron_variant chr22 43813408 rs5764317 0.00000222 SULT4A1 NR NR NR NA EFCAB6 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43823228 rs138053 0.00000222 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr22 43829914 rs138062 0.000000234 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43829993 rs138064 0.00000125 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43833612 rs138069 0.00000125 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43843619 rs138079 0.00000086 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43844805 rs470088 0.00000086 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43846187 rs80637 0.00000086 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43847894 rs138084 0.0000017 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43848422 rs138086 0.00000228 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43848741 rs138087 0.00000086 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43849201 rs80627 0.00000228 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43849299 rs80628 0.00000086 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43854690 rs138097 0.000000168 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43859952 rs138105 0.0000049 SULT4A1 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr22 43869595 rs138119 0.00000905 PNPLA5 NR NR NR NA SULT4A1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr22 43873442 rs138125 0.00000572 PNPLA5 NR NR NR NA PNPLA5 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr22 43876356 rs138127 0.00000239 PNPLA5 NR NR NR NA PNPLA5 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr22 43878322 rs129655 0.00000138 PNPLA5 NR NR NR NA PNPLA5 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker downstream_gene_variant chr22 43880291 rs470093 0.00000164 PNPLA5 NR NR NR NA PNPLA5 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker 3_prime_UTR_variant chr22 44958251 rs143258763 0.000000019 NR A A -2.41 0.0898153 PHF21B SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr22 44958251 rs143258763 0.00000002 NR A A -2.41 0.0898153 PHF21B SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr22 45368994 rs136564 2.11E-53 FAM118A NR NR 0.68 1.97388 SMC1B SNP-based eQTL 22685416 Caucasian MAYO 399 All FAM118A expression in Temporal cortex Expression intron_variant chr22 45368994 rs136564 3.74E-75 FAM118A NR NR 0.85 2.33965 SMC1B SNP-based eQTL 22685416 Caucasian MAYO 374 All FAM118A expression in Cerebellar Expression intron_variant chr22 45368994 rs136564 7.02E-39 FAM118A NR NR 0.82 2.2705 SMC1B SNP-based eQTL 22685416 Caucasian MAYO 197 AD FAM118A expression in Cerebellar Expression intron_variant chr22 45368994 rs136564 7.93E-30 FAM118A NR NR 0.88 2.4109 SMC1B SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD FAM118A expression in Cerebellar Expression intron_variant chr22 50521672 rs131814 0.0000086 NCAPH2 NR NR 0.249 1.28274 NCAPH2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr22 50521672 rs131814 0.000859 NCAPH2 NR NR 0.247 1.28018 NCAPH2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr22 50521672 rs131814 0.00236 NCAPH2 NR NR 0.257 1.29305 NCAPH2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr3 7243998 rs2007029 0.00000394 GRM7 NR NR NR NA GRM7 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intron_variant chr3 9437458 rs2442825 0.00000779 SETD5 NR NR 0.237 1.26744 SETD5 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr3 9437458 rs2442825 0.000475 SETD5 NR NR 0.261 1.29823 SETD5 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr3 9437458 rs2442825 0.0103 SETD5 NR NR 0.191 1.21046 SETD5 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr3 10092026 rs9849434 0.00000188 "FANCD2, FANCD2OS" A A 0.71 0.71 FANCD2 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr3 10093893 rs1552244 0.00000163 "FANCD2, FANCD2OS" G G 0.76 0.76 FANCD2 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intron_variant chr3 12355456 rs2881654 0.00000017 PPARG NR NR NR NA PPARG SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr3 28887369 rs2221154 0.00000258 NR T T 0.57 0.57 AC098650.1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intergenic_region chr3 32278916 rs7644602 0.0000395 CMTM8 NR NR 2.46 2.46 CMTM8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr3 32280107 rs11708149 0.0000401 CMTM8 NR NR 2.58 2.58 CMTM8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr3 32281483 rs6783478 0.0000397 CMTM8 NR NR 2.6 2.6 CMTM8 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr3 35101019 rs11129640 5.57E-08 ARPP-21 NR NR 0.124 1.13202 ARPP21 SNP-based Endophenotype 21116278 Caucasian "AddNeuroMed, ADNI" 939 All Entorhinal cortex thickness Imaging intergenic_region chr3 37193098 rs7631605 0.00000096 NR T T NR NA LRRFIP2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF P-tau181p Fluid biomarker upstream_gene_variant chr3 37732734 rs142726080 0.2 ITGA9 NR NR NR NA ITGA9 SNP-based Disease risk 25172201 African American ADGC 816 All AD AD missense_variant chr3 38126634 rs61095322 0.00736 ACAA1 C C NR NA ACAA1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD missense_variant chr3 38126634 rs61095322 1.27E-23 NR C C NR NA ACAA1 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group ACAA1 (ILMN_1738921) expression Expression missense_variant chr3 38126634 rs61095322 2.12E-10 NR A A NR NA ACAA1 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group ACAA1 (ENSG00000060971) expression Expression missense_variant chr3 39452367 rs9820623 0.0000169 MOBP NR NR NR NA MOBP SNP-based Cross phenotype 29630712 Caucasian "ALS group, IGAP, FTGC, AFTD, PSP Genetics Consortium, IPDGC" 36052 All AD AD intergenic_region chr3 39452367 rs9820623 0.0044 MOBP NR NR NR NA MOBP SNP-based Cross phenotype 29630712 Caucasian UKBEC NR All SCN11A expression in brain Expression intergenic_region chr3 39481512 rs1768208 0.000000171 MOBP NR NR 0.36 1.43333 MOBP SNP-based eQTL 22685416 Caucasian MAYO 374 All MOBP (ILMN_2298464) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.00000157 MOBP NR NR 0.33 1.39097 MOBP SNP-based eQTL 22685416 Caucasian MAYO 399 All MOBP (ILMN_2298464) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.0000176 MOBP NR NR 0.18 1.19722 MOBP SNP-based eQTL 22685416 Caucasian MAYO 399 All MOBP (ILMN_2414962) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.000117 MOBP NR NR 0.24 1.27125 MOBP SNP-based eQTL 22685416 Caucasian MAYO 374 All MOBP (ILMN_2414962) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.00037 MOBP NR NR 0.33 1.39097 MOBP SNP-based eQTL 22685416 Caucasian MAYO 197 AD MOBP (ILMN_2298464) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.00123 MOBP NR NR 0.31 1.36343 MOBP SNP-based eQTL 22685416 Caucasian MAYO 202 AD MOBP (ILMN_2298464) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.00303 MOBP NR NR 0.11 1.11628 MOBP SNP-based eQTL 22685416 Caucasian MAYO 399 All MOBP (ILMN_1768947) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.00757 MOBP NR NR 0.14 1.15027 MOBP SNP-based eQTL 22685416 Caucasian MAYO 374 All MOBP (ILMN_1768947) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.00818 MOBP NR NR 0.14 1.15027 MOBP SNP-based eQTL 22685416 Caucasian MAYO 202 AD MOBP (ILMN_2414962) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.0124 MOBP NR NR 0.34 1.40495 MOBP SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MOBP (ILMN_2298464) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0125 MOBP NR NR 0.2 1.2214 MOBP SNP-based eQTL 22685416 Caucasian MAYO 197 AD MOBP (ILMN_2414962) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0155 MOBP NR NR 0.05 1.05127 MOBP SNP-based eQTL 22685416 Caucasian MAYO 399 All MOBP (ILMN_1750271) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.0172 MOBP NR NR 0.16 1.17351 MOBP SNP-based eQTL 22685416 Caucasian MAYO 197 AD MOBP (ILMN_1768947) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0174 MOBP NR NR 0.24 1.27125 MOBP SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MOBP (ILMN_2414962) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.0183 MOBP NR NR 0.2 1.2214 MOBP SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MOBP (ILMN_1768947) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.0213 MOBP NR NR 0.07 1.07251 MOBP SNP-based eQTL 22685416 Caucasian MAYO 374 All MOBP (ILMN_1750271) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0233 MOBP NR NR 0.34 1.40495 MOBP SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MOBP (ILMN_2298464) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.0377 RPSA NR NR -0.06 0.941765 MOBP SNP-based eQTL 22685416 Caucasian MAYO 98 PSP RPSA (ILMN_2411723) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0429 MOBP NR NR 0.05 1.05127 MOBP SNP-based eQTL 22685416 Caucasian MAYO 202 AD MOBP (ILMN_1750271) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.0692 RPSA NR NR -0.03 0.970446 MOBP SNP-based eQTL 22685416 Caucasian MAYO 374 All RPSA (ILMN_2411723) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0802 MOBP NR NR 0.22 1.24608 MOBP SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MOBP (ILMN_2414962) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0872 RPSA NR NR -0.03 0.970446 MOBP SNP-based eQTL 22685416 Caucasian MAYO 197 AD RPSA (ILMN_2411723) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.0886 MOBP NR NR 0.07 1.07251 MOBP SNP-based eQTL 22685416 Caucasian MAYO 197 AD MOBP (ILMN_1750271) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.103 MOBP NR NR 0.08 1.08329 MOBP SNP-based eQTL 22685416 Caucasian MAYO 107 PSP MOBP (ILMN_1750271) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.138 MOBP NR NR 0.07 1.07251 MOBP SNP-based eQTL 22685416 Caucasian MAYO 202 AD MOBP (ILMN_1768947) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.147 SLC25A38 NR NR 0.03 1.03045 MOBP SNP-based eQTL 22685416 Caucasian MAYO 197 AD SLC25A38 (ILMN_1781231) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.284 BMS1 NR NR 0.02 1.0202 MOBP SNP-based eQTL 22685416 Caucasian MAYO 202 AD SLC25A38 (ILMN_1781231) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.284 MOBP NR NR 0.06 1.06184 MOBP SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MOBP (ILMN_1750271) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.433 SLC25A38 NR NR -0.02 0.980199 MOBP SNP-based eQTL 22685416 Caucasian MAYO 98 PSP SLC25A38 (ILMN_1781231) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.455 MOBP NR NR 0.08 1.08329 MOBP SNP-based eQTL 22685416 Caucasian MAYO 98 PSP MOBP (ILMN_1768947) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.729 RPSA NR NR -0.01 0.99005 MOBP SNP-based eQTL 22685416 Caucasian MAYO 107 PSP RPSA (ILMN_2411723) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.776 SLC25A38 NR NR 0 1 MOBP SNP-based eQTL 22685416 Caucasian MAYO 374 All SLC25A38 (ILMN_1781231) expression in Cerebellar Expression intron_variant chr3 39481512 rs1768208 0.902 SLC25A38 NR NR 0 1 MOBP SNP-based eQTL 22685416 Caucasian MAYO 399 All SLC25A38 (ILMN_1781231) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.941 RPSA NR NR 0 1 MOBP SNP-based eQTL 22685416 Caucasian MAYO 202 AD RPSA (ILMN_2411723) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.966 RPSA NR NR 0 1 MOBP SNP-based eQTL 22685416 Caucasian MAYO 399 All RPSA (ILMN_2411723) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 0.978 SLC25A38 NR NR 0 1 MOBP SNP-based eQTL 22685416 Caucasian MAYO 107 PSP SLC25A38 (ILMN_1781231) expression in Temporal cortex Expression intron_variant chr3 39481512 rs1768208 5.30E-17 MOBP NA NA 0.73 0.73 MOBP SNP-based Disease Risk 22685416 Caucasian "Cohorts from Europe, USA" 8851 All Progressive Supranuclear Palsy (PSP) ADRD intron_variant chr3 39708102 rs9832461 0.00000372 NR G G 3765.6 inf MYRIP SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr3 39708102 rs9832461 0.0000144 NR G G 3765.6 inf MYRIP SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr3 39730960 rs1527566 0.00000232 NR C C 3757.8 inf MYRIP SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr3 39730960 rs1527566 0.00000326 NR C C 3757.8 inf MYRIP SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr3 39755235 rs9878556 0.0000029 NR T T 3794.3 inf MYRIP SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr3 39755235 rs9878556 0.00000799 NR T T 3794.3 inf MYRIP SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr3 42530054 rs417387 0.00000279 VIPR1 NR NR 0.353 1.42333 VIPR1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr3 42530054 rs417387 0.00034 VIPR1 NR NR 0.37 1.44773 VIPR1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr3 42530054 rs417387 0.00273 VIPR1 NR NR 0.342 1.40776 VIPR1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr3 42864624 rs2228467 0.00225 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL2 Fluid biomarker missense_variant chr3 42864624 rs2228467 0.0482 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL2 Fluid biomarker missense_variant chr3 42864624 rs2228467 0.14 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker missense_variant chr3 42864624 rs2228467 0.51 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker missense_variant chr3 42864624 rs2228467 0.52 NA NR NR -0.021 0.979219 ACKR2 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD missense_variant chr3 42864624 rs2228467 0.8 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker missense_variant chr3 42864624 rs2228467 1.98E-08 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL2 Fluid biomarker missense_variant chr3 42864624 rs2228467 2.72E-10 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL2 Fluid biomarker missense_variant chr3 42864624 rs2228467 3.71E-18 CCBP2 G G NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL2 Fluid biomarker missense_variant chr3 42864624 rs2228467 5.36E-16 NA NR NR NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL2 Fluid biomarker missense_variant chr3 42864624 rs2228467 6.30E-12 CCBP2 G G NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL2 Fluid biomarker missense_variant chr3 42864624 rs2228467 7.42E-08 CCBP2 G G NR NA ACKR2 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL2 Fluid biomarker missense_variant chr3 44645808 rs1402752 0.00000869 NR NR NR NR NA ZNF197 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr3 44645808 rs1402752 0.000251 NR NR NR 2.64 2.64 ZNF197 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr3 44645808 rs1402752 0.000663 NR NR NR NR NA ZNF197 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr3 44645808 rs1402752 0.015 NR NR NR 1.48 1.48 ZNF197 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr3 44645808 rs1402752 0.643 NR NR NR NR NA ZNF197 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr3 44645808 rs1402752 0.809 NR NR NR NR NA ZNF197 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr3 44645808 rs1402752 0.81715 NR NR NR NR NA ZNF197 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr3 44645808 rs1402752 0.88493 NR NR NR NR NA ZNF197 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr3 44645808 rs1402752 1 NR NR NR 1.07 1.07 ZNF197 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr3 46358571 rs3092960 0.000000166 CCR2 G G NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL4 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.00000076 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL4 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.000002 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL4 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.00000404 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL4 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.0000236 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL4 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.0000265 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL4 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.0000504 CCR2 G G NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL4 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.6 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.679 NA NR NR 0.009 1.00904 CCR2 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD synonymous_variant chr3 46358571 rs3092960 0.89 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker synonymous_variant chr3 46358571 rs3092960 0.9 NA NR NR NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker synonymous_variant chr3 46358571 rs3092960 4.43E-11 CCR2 G G NR NA CCR2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL4 Fluid biomarker synonymous_variant chr3 46380864 rs11575821 0.000000299 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL4 Fluid biomarker intron_variant chr3 46380864 rs11575821 0.00000299 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46380864 rs11575821 0.0000114 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL4 Fluid biomarker intron_variant chr3 46380864 rs11575821 0.000105 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46380864 rs11575821 0.000242 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL4 Fluid biomarker intron_variant chr3 46380864 rs11575821 0.000642 CCR5 G G NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL4 Fluid biomarker intron_variant chr3 46380864 rs11575821 0.46 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr3 46380864 rs11575821 0.79 NA NR NR 0.006 1.00602 CCR5 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr3 46380864 rs11575821 0.96 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr3 46380864 rs11575821 0.98 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr3 46380864 rs11575821 1.13E-09 CCR5 G G NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL4 Fluid biomarker intron_variant chr3 46380864 rs11575821 1.22E-11 CCR5 G G NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.000000027 CCR5 G G NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.000000674 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.000000785 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.00000509 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.0000064 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.0000786 CCR5 G G NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.00012 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL4 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.53 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr3 46384227 rs113263161 0.74 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr3 46384227 rs113263161 0.83 NA NR NR 0.005 1.00501 CCR5 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr3 46384227 rs113263161 0.85 NA NR NR NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr3 46384227 rs113263161 1.41E-11 CCR5 G G NR NA CCR5 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.000000367 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.00000451 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.0000154 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.000048 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.00012 CCRL2 T T NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.000282 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.55 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr3 46405230 rs11574428 0.68 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr3 46405230 rs11574428 0.88 NA NR NR 0.003 1.003 CCRL2 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr3 46405230 rs11574428 0.93 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr3 46405230 rs11574428 1.48E-11 CCRL2 T T NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL4 Fluid biomarker intron_variant chr3 46405230 rs11574428 1.65E-08 CCRL2 T T NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL4 Fluid biomarker intron_variant chr3 46408373 rs6808835 0.000000286 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL4 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.000000307 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL4 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.00000888 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL4 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.0000297 CCRL2 G G NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL4 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.000196 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL4 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.47 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.53 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.64 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 0.81 NA NR NR 0.005 1.00501 CCRL2 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD synonymous_variant chr3 46408373 rs6808835 1.59E-13 CCRL2 G G NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL4 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 5.35E-10 CCRL2 G G NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL4 Fluid biomarker synonymous_variant chr3 46408373 rs6808835 8.13E-09 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL4 Fluid biomarker synonymous_variant chr3 46408581 rs6441977 0.000000113 CCRL2 G G NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL4 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.000000763 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL4 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.00000726 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL4 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.0000363 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL4 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.000113 CCRL2 G G NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL4 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.000201 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL4 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.000668 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL4 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.41 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker missense_variant chr3 46408581 rs6441977 0.59 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker missense_variant chr3 46408581 rs6441977 0.8 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker missense_variant chr3 46408581 rs6441977 0.81 NA NR NR 0.006 1.00602 CCRL2 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD missense_variant chr3 46408581 rs6441977 7.66E-11 CCRL2 G G NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL4 Fluid biomarker missense_variant chr3 46411372 rs6762266 0.000000184 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46411372 rs6762266 0.000000684 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 No amyloid deposition strata CSF CCL4 Fluid biomarker intron_variant chr3 46411372 rs6762266 0.00000888 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR > 0 CSF CCL4 Fluid biomarker intron_variant chr3 46411372 rs6762266 0.0000407 CCRL2 C C NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian ADNI 308 All CSF CCL4 Fluid biomarker intron_variant chr3 46411372 rs6762266 0.000159 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All Plasma CCL4 Fluid biomarker intron_variant chr3 46411372 rs6762266 0.58 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF P-tau181p Fluid biomarker intron_variant chr3 46411372 rs6762266 0.59 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF Ab1-42 Fluid biomarker intron_variant chr3 46411372 rs6762266 0.64 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF T-tau Fluid biomarker intron_variant chr3 46411372 rs6762266 0.7 NA NR NR 0.009 1.00904 CCRL2 SNP-based Disease risk 25340798 Caucasian IGAP 54162 All AD AD intron_variant chr3 46411372 rs6762266 1.25E-08 NA NR NR NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 Subjects with CDR = 0 CSF CCL4 Fluid biomarker intron_variant chr3 46411372 rs6762266 2.27E-13 CCRL2 C C NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian "ADNI, Knight-ADRC" 574 All CSF CCL4 Fluid biomarker intron_variant chr3 46411372 rs6762266 5.35E-10 CCRL2 C C NR NA CCRL2 SNP-based Endophenotype 25340798 Caucasian Knight-ADRC 266 All CSF CCL4 Fluid biomarker intron_variant chr3 52550771 rs2251219 0.28 PBRM1 NR NR 1.06 1.06 SMIM4 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD synonymous_variant chr3 52550771 rs2251219 0.95 PBRM1 NR NR 1 1 SMIM4 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD synonymous_variant chr3 54319213 rs7431992 1.99E-08 CACNA2D3 A A 1.59 1.59 CACNA2D3 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr3 54319213 rs7431992 5.80E-09 CACNA2D3 A A 1.61 1.61 CACNA2D3 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr3 56705895 rs6805910 0.00061 ARHGEF3 C C NR NA ARHGEF3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr3 56705895 rs6805910 0.000693 ARHGEF3 C C NR NA ARHGEF3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intergenic_region chr3 56705895 rs6805910 0.718 ARHGEF3 C C 1 1 ARHGEF3 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr3 57192122 rs184384746 1.24E-08 HESX1 T T 5.69 NA HESX1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intergenic_region chr3 59905250 rs643629 0.00000998 NR A A NR NA FHIT SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr3 59907310 rs624225 0.00000512 NR C C NR NA FHIT SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr3 64941350 rs704454 0.0000026 ADAMTS9 NR NR NR NA ADAMTS9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr3 64941350 rs704454 0.0000046 ADAMTS9 NR NR 1.22 3.38719 ADAMTS9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intron_variant chr3 64941350 rs704454 0.0000155 ADAMTS9 NR NR NR NA ADAMTS9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr3 64941350 rs704454 0.0832 ADAMTS9 NR NR 0.5 1.64872 ADAMTS9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intron_variant chr3 64941350 rs704454 0.154 ADAMTS9 NR NR 2.94 18.9158 ADAMTS9 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intron_variant chr3 66855351 rs9862849 0.00000266 KBTBD8 C C 0.6 0.6 KBTBD8 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intergenic_region chr3 67406609 rs62256378 0.000000015 NR A A 0.97 2.63794 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with APOE-e4 non-carrier CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.0000003 NR A A 0.61 1.84043 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.0000019 NR A A 0.61 1.84043 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.000025 NR A A 2.13 8.41487 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 113 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.00011 NR A A 0.94 2.55998 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe NR AD subjects with APOE-e4 non-carrier CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.0006 NR A A 0.82 2.2705 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 167 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.0015 NR A A 0.35 1.41907 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with heterozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.0031 NR A A 0.32 1.37713 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.0048 NR A A 1.68 5.36556 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with APOE-e4 non-carrier CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.0088 NR A A 0.96 2.6117 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with APOE-e4 non-carrier CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.02 NR A A 0.61 1.84043 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe NR AD subjects with APOE-e4 non-carrier MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.021 NR A A 0.32 1.37713 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with APOE-e4 non-carrier MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.03 NR A A 0.32 1.37713 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe NR AD subjects with heterozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.04 NR A A 0.45 1.56831 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with heterozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.072 NR A A 0.31 1.36343 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with heterozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.08 NR A A 0.28 1.32313 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.08 NR A A 0.57 1.76827 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 113 AD subjects MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.09 NR A A 0.5 1.64872 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI 83 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.11 NR A A 0.24 1.27125 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI 83 AD subjects MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.14 NR A A 0.66 1.93479 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI NR AD subjects with APOE-e4 non-carrier CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.14 NR A A 1.23 3.42123 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI NR AD subjects with homozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.141 NR A A 0.4 1.49182 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with homozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.15 NR A A 0.43 1.53726 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI NR AD subjects with heterozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.15 NR A A 0.66 1.93479 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 167 AD subjects MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.16 NR A A 1.07 2.91538 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with heterozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.23 NR A A 0.57 1.76827 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with APOE-e4 non-carrier MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.25 NR A A 0.38 1.46228 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with heterozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.25 NR A A 1.38 3.9749 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with homozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.26 NR A A 0.29 1.33643 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe NR AD subjects with homozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.29 NR A A 0.18 1.19722 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe NR AD subjects with heterozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.33 NR A A 0.48 1.61607 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI NR AD subjects with heterozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.39 NR A A 0.26 1.29693 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with APOE-e4 non-carrier MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.44 NR A A 0.24 1.27125 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with heterozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.5 NR A A 0.01 1.01005 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI NR AD subjects with APOE-e4 non-carrier MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 0.71 NR A A -0.13 0.878095 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with homozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.83 NR A A -0.04 0.960789 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with homozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.9 NR A A -0.1 0.904837 SUCLG2 SNP-based Endophenotype 25027320 Caucasian ADNI NR AD subjects with homozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 0.96 NR A A 0.01 1.01005 SUCLG2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe NR AD subjects with homozygous APOE-e4 CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 1 NR A A -0.36 0.697676 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" NR AD subjects with homozygous APOE-e4 MMSE Score Cognitive intron_variant chr3 67406609 rs62256378 2.50E-12 NR A A 0.71 2.03399 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 67406609 rs62256378 2.50E-12 NR A A 0.71 2.03399 SUCLG2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 85835000 rs13078807 0.236 NR G G 0.969 0.969 CADM2 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr3 85835000 rs13078807 0.675 NR G G 0.982 0.982 CADM2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr3 85835000 rs13078807 0.912 NR G G 1.01 1.01 CADM2 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr3 85835000 rs13078807 0.953 NR G G 0 1 CADM2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr3 104209719 rs74528420 0.00000442 MIR548AB T T 0.72 0.72 ALCAM SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD intergenic_region chr3 104241993 rs28868104 0.000000351 MIR548AB C C 0.69 0.69 ALCAM SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD intergenic_region chr3 104256947 rs4501143 0.00000123 MIR548AB T T 1.44 1.44 ALCAM SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD intergenic_region chr3 107825799 rs2029773 0.00000812 LINC00635 NR NR NR NA BBX SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr3 113103475 rs9811423 0.00000418 RP11-572M11.4 NR NR 1.28 1.28 NEPRO SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intron_variant chr3 122066784 rs2681411 0.0000421 CD86 NR NR NR NA CD86 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr3 128617674 rs2811488 0.0000105 "FLJ40473, RPN1" NR NR NR NA RPN1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD downstream_gene_variant chr3 132225793 rs11714139 0.000000125 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132225793 rs11714139 0.000481 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132225793 rs11714139 5.41E-10 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132226007 rs56226080 0.000000125 ACPP C C NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132226007 rs56226080 0.000481 ACPP C C NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132226007 rs56226080 5.41E-10 ACPP C C NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132229196 rs73211958 0.000000125 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132229196 rs73211958 0.000511 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132229196 rs73211958 5.82E-10 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132288366 rs11706024 1.71E-12 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132288366 rs11706024 3.62E-08 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132288366 rs11706024 6.40E-19 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132291037 rs16839055 0.0000249 ACPP T T NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132291037 rs16839055 0.000252 ACPP T T NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132291037 rs16839055 2.55E-08 ACPP T T NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132296965 rs2887519 1.71E-12 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132296965 rs2887519 3.62E-08 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132296965 rs2887519 6.40E-19 ACPP A A NR NA CPNE4 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132305299 rs113143077 1.71E-12 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132305299 rs113143077 3.62E-08 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132305299 rs113143077 6.40E-19 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132313089 rs73213842 1.71E-12 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132313089 rs73213842 3.62E-08 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132313089 rs73213842 6.40E-19 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132314846 rs17344445 1.71E-12 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132314846 rs17344445 3.62E-08 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132314846 rs17344445 6.40E-19 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132315355 rs3844501 1.74E-20 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132315355 rs3844501 1.97E-13 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132315355 rs3844501 7.97E-09 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132315535 rs3762671 1.52E-19 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132315535 rs3762671 3.25E-08 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132315535 rs3762671 3.82E-13 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132317103 rs56030168 0.00000134 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132317103 rs56030168 2.94E-11 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132317103 rs56030168 4.65E-16 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker upstream_gene_variant chr3 132323221 rs56073503 1.71E-12 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132323221 rs56073503 3.62E-08 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132323221 rs56073503 6.40E-19 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132323245 rs56158166 1.71E-12 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132323245 rs56158166 3.62E-08 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132323245 rs56158166 6.40E-19 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132326151 rs11716607 1.71E-12 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132326151 rs11716607 3.62E-08 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132326151 rs11716607 6.40E-19 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132343273 rs4257547 0.0000519 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132343273 rs4257547 0.000194 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132343273 rs4257547 3.87E-08 ACPP G G NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132347347 rs11928839 0.0000649 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132347347 rs11928839 0.00016 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132347347 rs11928839 3.93E-08 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132347415 rs11917521 0.0000649 ACPP C C NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132347415 rs11917521 0.00016 ACPP C C NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132347415 rs11917521 3.93E-08 ACPP C C NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132356006 rs17182812 0.0000649 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132356006 rs17182812 0.000139 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132356006 rs17182812 3.43E-08 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intron_variant chr3 132356902 rs1042330 0.0000649 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132356902 rs1042330 0.000139 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132356902 rs1042330 3.43E-08 ACPP A A NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132357707 rs14192 0.000048 ACPP C C NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132357707 rs14192 0.000139 ACPP C C NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132357707 rs14192 2.57E-08 ACPP C C NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132357862 rs1804136 0.000048 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132357862 rs1804136 0.000139 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132357862 rs1804136 2.57E-08 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker 3_prime_UTR_variant chr3 132379021 rs3889987 0.000000408 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian Knight-ADRC 246 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132379021 rs3889987 1.77E-18 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian "ADNI, Knight-ADRC" 543 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 132379021 rs3889987 2.15E-13 ACPP T T NR NA ACP3 SNP-based Cross phenotype 27357282 Caucasian ADNI 297 All CSF Prostatic Acid Phosphatase (PAP) Fluid biomarker intergenic_region chr3 133775510 rs1049296 0.242 TF T T 1.12 1.12 TF SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD missense_variant chr3 137931894 rs16847609 0.00000023 "CLDN18, SOX14" A A 1.21 1.21 CLDN18 SNP-based Disease risk 25778476 Caucasian IGAP 34152 APOE-e4- subjects AD AD intergenic_region chr3 137931894 rs16847609 0.00000053 "CLDN18, SOX14" A A 1.19 1.19 CLDN18 SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD intergenic_region chr3 137931894 rs16847609 0.47 "CLDN18, SOX14" A A 1.09 1.09 CLDN18 SNP-based Disease risk 25778476 Caucasian ADGC 2417 APOE-e4- subjects AD AD intergenic_region chr3 139531807 rs893703 0.0000012 NR G G 0.89 2.43513 RBP1 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 139531807 rs893703 0.0032 NR G G 0.25 1.28403 RBP1 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 139536170 rs4407373 0.68 NR T T -0.05 0.951229 RBP1 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 139559716 rs4564921 0.00000612 NMNAT3 C C 0.14 1.15027 NMNAT3 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intron_variant chr3 139804291 rs952797 0.000000028 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All "Cognitive function (Memory - Learning (or working memory), Memory - Delayed recall, Memory - Recognition, Executive Function - Stroop Color Word test, Executive Function - Part B of the Trail making test (TMTB), Executive Function - Block test, Verbal Fluency - Semantic fluency, Verbal Fluency - Phonological fluency)" Cognitive intergenic_region chr3 139804291 rs952797 0.0002 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Block test Cognitive intergenic_region chr3 139804291 rs952797 0.05 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Stroop Color Word test Cognitive intergenic_region chr3 139804291 rs952797 0.06 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Learning (or working memory) Cognitive intergenic_region chr3 139804291 rs952797 0.24 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Phonological fluency Cognitive intergenic_region chr3 139804291 rs952797 0.47 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Delayed recall Cognitive intergenic_region chr3 139804291 rs952797 0.57 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Memory - Recognition Cognitive intergenic_region chr3 139804291 rs952797 0.82 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Verbal Fluency - Semantic fluency Cognitive intergenic_region chr3 139804291 rs952797 0.89 "NMNAT3, CLSTN2" NA NA NA NA NMNAT3 SNP-based Endophenotype 17564960 genetically isolated community in the southwestern area of The Netherlands GRIP 197 All Executive Function - Part B of the Trail making test (TMTB) Cognitive intergenic_region chr3 153652877 rs11711889 0.00000695 NR NR NR NR NA ARHGEF26 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr3 153652877 rs11711889 0.000165 NR NR NR 0.5 0.5 ARHGEF26 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr3 153652877 rs11711889 0.000175 NR NR NR NR NA ARHGEF26 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr3 153652877 rs11711889 0.00365 NR NR NR 0.49 0.49 ARHGEF26 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr3 153652877 rs11711889 0.0225 NR NR NR NR NA ARHGEF26 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr3 153652877 rs11711889 0.0381 NR NR NR NR NA ARHGEF26 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr3 153652877 rs11711889 0.383 NR NR NR 0.52 0.52 ARHGEF26 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr3 153652877 rs11711889 0.49535 NR NR NR NR NA ARHGEF26 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr3 153652877 rs11711889 NA NR NR NR NR NA ARHGEF26 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr3 155317962 rs114816986 0.00000197 NR A A NR NA STRIT1 SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intergenic_region chr3 158324919 rs144747720 0.00288 RSRC1 NR NR NR NA RSRC1 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr3 158324919 rs144747720 0.8971 NA NR NR NR NA RSRC1 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr3 158605927 rs7617983 0.112 MLF1 NR NR NR NA MLF1 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr3 158605927 rs7617983 0.51648 NA NR NR NR NA MLF1 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr3 160234491 rs6441306 0.00000122 IFT80 NR NR NR NA AC079594.2 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr3 165567101 rs12493397 0.0000039 NR A A 0.64 1.89648 BCHE SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 165567101 rs12493397 0.0012 NR A A -0.18 0.83527 BCHE SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 165571636 rs2222464 0.76 NR C C -0.02 0.980199 BCHE SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr3 178442780 rs12492269 0.00000222 LINC01014 NR NR NR NA KCNMB2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intron_variant chr3 178796465 rs73183328 0.000082 KCNMB2 A A 2.42 2.42 KCNMB2 SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (ADD Model) Hippocampal sclerosis of aging ADRD intron_variant chr3 178796465 rs73183328 0.00016 KCNMB2 NR NR 2.4 2.4 KCNMB2 SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (DOM Model) Hippocampal sclerosis of aging ADRD intron_variant chr3 178806917 rs13091964 0.011 KCNMB2 T T 1.84 1.84 KCNMB2 SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (REC Model) Hippocampal sclerosis of aging ADRD intron_variant chr3 185787999 rs4481184 3.20E-10 IGF2BP2 NR NR NR NA IGF2BP2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr3 185795604 rs7651090 2.00E-11 IGF2BP2 NR NR NR NA IGF2BP2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr3 186116710 rs9816226 0.283 NR T T 0.004 1.00401 DGKG SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr3 186116710 rs9816226 0.391 NR T T 1.041 1.041 DGKG SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr3 186116710 rs9816226 0.449 NR T T 1.041 1.041 DGKG SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr3 186618152 rs2070633 0.00406 AHSG NR NR -181.75 1.16675e-79 AHSG SNP-based Endophenotype 23894628 Non-Hispanic Caucasian IMAS 59 All Plasma Fetuin-A Fluid biomarker intron_variant chr3 186618152 rs2070633 4.50E-31 AHSG NR NR -0.06 0.941765 AHSG SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma Fetuin-A Fluid biomarker intron_variant chr3 190889174 rs1393060 0.03 GLIS1 NR NR 0.02 1.0202 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF T-tau Fluid biomarker intron_variant chr3 190889174 rs1393060 0.047 GLIS1 NR NR 0.14 1.15027 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 704 Female AD subjects Neuronal Neurofibrillary Tangles Neuropathology intron_variant chr3 190889174 rs1393060 0.93 GLIS1 NR NR 0.01 1.01005 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 362 Male AD subjects Neuronal Neurofibrillary Tangles Neuropathology intron_variant chr3 190889174 rs1393060 4.57E-10 GLIS1 NR NR 0.05 1.05127 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF T-tau Fluid biomarker intron_variant chr3 190939374 rs1316356 0.000000196 SNAR-I NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr3 190939374 rs1316356 0.00000028 SNAR-I NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr3 190939374 rs1316356 0.102 SNAR-I NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intergenic_region chr3 190945768 rs35055419 0.00000148 GLIS1 NR NR 0.04 1.04081 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF P-tau181p Fluid biomarker intergenic_region chr3 190945768 rs35055419 0.0002 GLIS1 NR NR 0.03 1.03045 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF P-tau181p Fluid biomarker intergenic_region chr3 190945768 rs35055419 0.0003 GLIS1 NR NR 0.03 1.03045 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF T-tau Fluid biomarker intergenic_region chr3 190945768 rs35055419 0.00314 GLIS1 C C 0.04 1.04081 GMNC SNP-based Age at onset (AAO) / Survival 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 39855 AD subjects Age at onset Other intergenic_region chr3 190945768 rs35055419 0.00908 GLIS1 C C 1.04 2.82922 GMNC SNP-based Disease risk 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 74046 All AD risk AD intergenic_region chr3 190945768 rs35055419 0.0971 GLIS1 C C 0.007 1.00702 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF Ab1-42 Fluid biomarker intergenic_region chr3 190945768 rs35055419 0.525 GLIS1 C C 0.03 1.03045 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1530 All AD Progression (based on CDR Score) Cognitive intergenic_region chr3 190945768 rs35055419 2.57E-08 GLIS1 NR NR 0.05 1.05127 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF T-tau Fluid biomarker intergenic_region chr3 190945768 rs35055419 3.07E-11 GLIS1 C C 0.04 1.04081 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF T-tau Fluid biomarker intergenic_region chr3 190945768 rs35055419 3.07E-11 GLIS1 NR NR 0.04 1.04081 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF T-tau Fluid biomarker intergenic_region chr3 190945768 rs35055419 7.62E-10 GLIS1 C C 0.04 1.04081 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF P-tau181p Fluid biomarker intergenic_region chr3 190945768 rs35055419 7.62E-10 GLIS1 NR NR 0.04 1.04081 GMNC SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF P-tau181p Fluid biomarker intergenic_region chr3 190951729 rs9877502 0.000000168 SNAR-I NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr3 190951729 rs9877502 0.000000247 NR NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr3 190951729 rs9877502 0.00000046 NR NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr3 190951729 rs9877502 0.000000562 NR NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr3 190951729 rs9877502 0.000000724 NR NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr3 190951729 rs9877502 0.0000464 NR A A -0.014 0.986098 GMNC SNP-based Cognitive 23562540 NR ROSMAP 1593 All global cognitive decline Cognitive intergenic_region chr3 190951729 rs9877502 0.000267 NR A A 0.081 1.08437 GMNC SNP-based Disease risk 23562540 Caucasian ADGC 22771 All AD AD intergenic_region chr3 190951729 rs9877502 0.014 NR A A 0.055 1.05654 GMNC SNP-based Neuropathology 23562540 NR ROSMAP 651 All tangle counts Neuropathology intergenic_region chr3 190951729 rs9877502 0.022 SNAR-I NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intergenic_region chr3 190951729 rs9877502 4.39E-08 NR NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr3 190951729 rs9877502 4.98E-09 SNAR-I NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr3 190951729 rs9877502 7.77E-09 NR NR NR NR NA GMNC SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr3 190953113 rs9811910 0.01 NR C C 0.08 1.08329 GMNC SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 2363 European Intracranial Volume Imaging intergenic_region chr3 190953113 rs9811910 0.02 NR C C 0.35 1.41907 GMNC SNP-based Endophenotype 27694991 African American "CHARGE, ENIGMA" 938 African Intracranial Volume Imaging intergenic_region chr3 190953113 rs9811910 0.187 NR C C -0.15 0.860708 GMNC SNP-based Endophenotype 27694991 Hispanic "CHARGE, ENIGMA" 1605 Hispanic Intracranial Volume Imaging intergenic_region chr3 190953113 rs9811910 0.621 NR C C 0.1 1.10517 GMNC SNP-based Endophenotype 27694991 Asian "CHARGE, ENIGMA" 955 Asian Intracranial Volume Imaging intergenic_region chr3 190953113 rs9811910 1.20E-09 NR C C 0.1 1.10517 GMNC SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 26577 European Intracranial Volume Imaging intergenic_region chr4 864544 rs11248051 0.000000035 GAK T T NR NA GAK SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intron_variant chr4 864544 rs11248051 0.19 GAK T T NR NA GAK SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intron_variant chr4 1166078 rs111388896 0.00515 UVSSA C C NR NA SPON2 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD upstream_gene_variant chr4 1166078 rs111388896 2.27E-24 NR C C NR NA SPON2 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group UVSSA (ENSG00000163945) expression Expression upstream_gene_variant chr4 1297549 rs3817604 0.00041 CRIPAK T T NR NA MAEA SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr4 1297549 rs3817604 1.14E-09 NR T T NR NA MAEA SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) CRIPAK expression in Hippocampus Expression intron_variant chr4 1297549 rs3817604 5.77E-10 NR T T NR NA MAEA SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) SFN (ILMN_1806607) expression Expression intron_variant chr4 2101369 rs1923775 0.00000561 POLN T T 1.6 1.6 POLN SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr4 5095813 rs17675640 0.00000189 STK32B G G 0.77 0.77 STK32B SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr4 5096839 rs6838792 0.00000161 STK32B C C 0.77 0.77 STK32B SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr4 5099404 rs895681 0.00000272 STK32B T T 0.78 0.78 STK32B SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr4 6265274 rs4688982 0.0000014 "LOC285484, WFS1" NR NR NR NA WFS1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD upstream_gene_variant chr4 6265360 rs4688983 0.0000053 WFS1 NR NR NR NA WFS1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD upstream_gene_variant chr4 6301627 rs734312 0.00000032 WFS1 NR NR NR NA WFS1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD missense_variant chr4 7283629 rs3846421 0.000117 SORCS2 NR NR NR NA SORCS2 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr4 7283629 rs3846421 0.00313 SORCS2 NR NR NR NA SORCS2 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr4 7283629 rs3846421 0.0206 SORCS2 NR NR NR NA SORCS2 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr4 7312316 rs11722747 0.0484 SORCS2 A A 0.06 1.06184 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7324472 rs4689707 0.0434 SORCS2 T T 0.07 1.07251 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7326689 rs3864203 0.0364 SORCS2 A A 0.0554 1.05696 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7327007 rs7665496 0.0118 SORCS2 T T 0.1045 1.11016 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7327338 rs7661158 0.0372 SORCS2 A A 0.0497 1.05096 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7327597 rs6840423 0.0172 SORCS2 T T 0.08 1.08329 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7327699 rs3864202 0.0351 SORCS2 A A 0.049 1.05022 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7328949 rs16840053 0.0136 SORCS2 A A 0.08 1.08329 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7351325 rs13110208 0.00944 SORCS2 T T 0.0626 1.0646 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7388715 rs4689720 0.0264 SORCS2 T T 0.1178 1.12502 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7415514 rs7684383 0.0384 SORCS2 T T 0.1429 1.15361 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7415905 rs4234804 0.0251 SORCS2 A A 0.1509 1.16288 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7417549 rs6837589 0.0336 SORCS2 T T 0.0589 1.06067 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7418457 rs13105690 0.0155 SORCS2 T T 0.0599 1.06173 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7419058 rs4292336 0.049 SORCS2 A A 0.05 1.05127 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7620620 rs17465564 0.0315 SORCS2 A A 0.09 1.09417 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7665759 rs2214459 0.0265 SORCS2 T T 0.0519 1.05327 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 7732116 rs12233824 0.0488 SORCS2 A A 0.04 1.04081 SORCS2 SNP-based Disease risk 23673467 Caucasian ADGC 22771 All AD AD intron_variant chr4 8377136 rs62286001 0.00549 ACOX3 C C NR NA ACOX3 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr4 8377136 rs62286001 7.84E-14 NR C C NR NA ACOX3 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group ACOX3 (ENSG00000087008) expression Expression intron_variant chr4 10048517 rs733175 0.00000497 SLC2A9 NR NR 1.37 1.37 SLC2A9 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intron_variant chr4 10060702 rs6834555 0.000000306 SLC2A9 NR NR 1.4 1.4 SLC2A9 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intergenic_region chr4 11023058 rs6448451 1.19E-08 CLNK A A NR NA CLNK SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intergenic_region chr4 11024404 rs6448453 0.024 CLNK A A NR NA CLNK SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intergenic_region chr4 11024404 rs6448453 1.93E-09 CLNK A A 6 NA CLNK SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intergenic_region chr4 11628425 rs6448799 0.901 HS3ST1 T T 0.994 0.994 HS3ST1 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr4 11709608 rs13113697 0.000000503 HS3ST1 T T 1.07 1.07 HS3ST1 SNP-based Disease risk 25862742 Caucasian IGAP 74046 All AD AD intron_variant chr4 11709608 rs13113697 0.031 HS3ST1 T T 1.07 1.07 HS3ST1 SNP-based Disease risk 25862742 Caucasian deCODE 67817 All AD AD intron_variant chr4 11709608 rs13113697 0.088 HS3ST1 T T 1.13 1.13 HS3ST1 SNP-based Disease risk 25862742 Caucasian DemGene 2015 All AD AD intron_variant chr4 11709608 rs13113697 2.86E-08 HS3ST1 T T 1.07 1.07 HS3ST1 SNP-based Disease risk 25862742 Caucasian "deCODE, DemGene, IGAP" 143878 All AD AD intron_variant chr4 11721611 rs7657553 0.051 HS3ST1 A A 1.95 NA HS3ST1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr4 11721611 rs7657553 0.79 HS3ST1 A A NR NA HS3ST1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr4 11721611 rs7657553 2.16E-08 HS3ST1 A A NR NA HS3ST1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr4 15735725 rs4698412 0.031 BST1 G G NR NA BST1 SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intron_variant chr4 15735725 rs4698412 2.03E-08 BST1 A A NR NA BST1 SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intron_variant chr4 20759888 rs6817475 0.00000038 KCNIP4 G G 0.17 1.1853 KCNIP4 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intron_variant chr4 25248350 rs313561 0.5 NR G G -0.06 0.941765 PI4K2B SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr4 25261856 rs313541 0.0000028 NR G G 0.5 1.64872 PI4K2B SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr4 25261856 rs313541 0.013 NR G G 0.16 1.17351 PI4K2B SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr4 30466544 rs6856768 0.00000463 NR NR NR 0.85 0.85 PCDH7 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intergenic_region chr4 30466544 rs6856768 0.0000822 NR NR NR NR NA PCDH7 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intergenic_region chr4 30466544 rs6856768 0.00305 NR NR NR 0.81 0.81 PCDH7 SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD intergenic_region chr4 30466544 rs6856768 0.00311 NR NR NR 0.82 0.82 PCDH7 SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD intergenic_region chr4 30466544 rs6856768 0.0819 NR NR NR 0.89 0.89 PCDH7 SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD intergenic_region chr4 30466544 rs6856768 0.12 NR NR NR 0.88 0.88 PCDH7 SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD intergenic_region chr4 30466544 rs6856768 0.855 NR NR NR 0.97 0.97 PCDH7 SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD intergenic_region chr4 33078033 rs1448284 0.00000132 NR C C 9939.9 inf PCDH7 SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr4 33078033 rs1448284 0.00000196 NR C C 9939.9 inf PCDH7 SNP-based Endophenotype 20197096 Caucasian ADNI 742 All Temporal Lobe Atrophy Imaging intergenic_region chr4 33201518 rs10517270 0.00000413 NR NR NR NR NA PCDH7 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intergenic_region chr4 33201518 rs10517270 0.00000587 NR NR NR NR NA PCDH7 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intergenic_region chr4 33201518 rs10517270 0.000267 NR NR NR -3.31 0.0365162 PCDH7 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intergenic_region chr4 33201518 rs10517270 0.0113 NR NR NR -3.95 0.0192547 PCDH7 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intergenic_region chr4 33201518 rs10517270 0.0408 NR NR NR -18.66 7.87164e-09 PCDH7 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intergenic_region chr4 42410670 rs12639920 0.0000485 ATP8A1 NR NR NR NA ATP8A1 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD 3_prime_UTR_variant chr4 45180510 rs10938397 0.117 NR G G 1.041 1.041 GNPDA2 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr4 45180510 rs10938397 0.2 NR G G 1.062 1.062 GNPDA2 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr4 45180510 rs10938397 0.363 NR G G 0 1 GNPDA2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr4 45180510 rs10938397 0.93 NR G G 1 1 GNPDA2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr4 47790280 rs59776273 0.000099 CORIN NR NR NR NA CORIN SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intron_variant chr4 47790280 rs59776273 0.00019 CORIN NR NR NR NA CORIN SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intron_variant chr4 47790280 rs59776273 0.00044 CORIN NR NR NR NA CORIN SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intron_variant chr4 47790280 rs59776273 0.032 CORIN NR NR NR NA CORIN SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intron_variant chr4 48998833 rs6850199 0.000000318 FLJ21511 A A NR NA CWH43 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF T-tau Fluid biomarker intron_variant chr4 49027884 rs2768975 0.000000196 FLJ21511 G G NR NA CWH43 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF T-tau Fluid biomarker intron_variant chr4 55802265 rs753129 0.000000285 AC110611.1 NR NR 0.66 0.66 EXOC1L SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD downstream_gene_variant chr4 60905713 rs1455280 0.0001 Intergenic (as reported in paper) G G NR NA ADGRL3 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr4 60905713 rs1455280 0.00027 NR G G NR NA ADGRL3 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr4 60905713 rs1455280 0.0026 NR G G NR NA ADGRL3 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr4 67684577 rs13114818 0.000628 UBA6 C C NR NA UBA6 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr4 67684577 rs13114818 0.000896 UBA6 C C NR NA UBA6 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr4 67684577 rs13114818 0.00303 UBA6 C C 1.05 1.05 UBA6 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr4 67684577 rs13114818 0.0075 UBA6 C C 1.05 1.05 UBA6 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr4 67684577 rs13114818 0.408 UBA6 C C 0.94 0.94 UBA6 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr4 67684577 rs13114818 0.44 UBA6 C C 1 1 UBA6 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr4 72095821 rs12510838 0.00024 NPFFR2 G G NR NA NPFFR2 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 72095821 rs12510838 0.0008 NPFFR2 G G NR NA NPFFR2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 72095821 rs12510838 0.0047 NPFFR2 G G NR NA NPFFR2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 73455883 rs10020432 0.0000226 AFP NR NR -0.07 0.932394 AFP SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma AFP Fluid biomarker 3_prime_UTR_variant chr4 76031127 rs6852075 0.000402 ART3 G G NR NA ART3 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr4 76031127 rs6852075 0.000517 ART3 G G NR NA ART3 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total triglycerides (TG) Non-ADRD intron_variant chr4 76031127 rs6852075 0.0177 ART3 G G 0.97 0.97 ART3 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr4 76031127 rs6852075 0.0196 ART3 G G 0.97 0.97 ART3 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr4 76031127 rs6852075 0.623 ART3 G G 0.98 0.98 ART3 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr4 76166551 rs7664889 0.000175 SCARB2 NR NR NR NA SCARB2 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr4 76166551 rs7664889 0.000175 SCARB2 T T 0.73 0.73 SCARB2 SNP-based Disease risk 27899424 Caucasian IFGC 6462 All Frontotemporal Dementia ADRD intron_variant chr4 76166551 rs7664889 0.00318 SCARB2 T T 0.83 0.83 SCARB2 SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr4 76166551 rs7664889 0.82 SCARB2 T T 0.98 0.98 SCARB2 SNP-based Disease risk 27899424 Caucasian IFGC 6466 All Frontotemporal Dementia ADRD intron_variant chr4 76189212 rs6825004 0.42 SCARB2 NR NR 0.92 0.92 SCARB2 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr4 85495401 rs111882035 2.74E-08 ARHGAP24 G G -0.93 0.394554 ARHGAP24 SNP-based Endophenotype 29274321 Caucasian ADNI 581 MCI Logic memory delayed (LMdT) recall test Cognitive intron_variant chr4 89720189 rs356220 0.014 SNCA C C NR NA SNCA SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intron_variant chr4 89720189 rs356220 1.47E-25 SNCA T T NR NA SNCA SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intron_variant chr4 89754087 rs3857059 0.78 SNCA A A NR NA SNCA SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intron_variant chr4 89754087 rs3857059 1.66E-14 SNCA G G NR NA SNCA SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intron_variant chr4 89808451 rs2197120 0.99 SNCA G G NR NA SNCA SNP-based Disease risk 25687773 Caucasian ADGC 22771 All AD AD intron_variant chr4 89808451 rs2197120 6.29E-10 SNCA G G NR NA SNCA SNP-based Disease risk 25687773 Caucasian IPDGC 17352 All PD ADRD intron_variant chr4 89843548 rs7687945 0.92 SNCA NR NR 1 1 SNCA SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging downstream_gene_variant chr4 94421638 rs4699852 0.00004 NR A A NR NA PDLIM5 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr4 94421638 rs4699852 0.0008 Intergenic (as reported in paper) A A NR NA PDLIM5 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr4 94421638 rs4699852 0.0032 NR A A NR NA PDLIM5 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr4 95238666 rs12643654 0.000000495 UNC5C G G NR NA UNC5C SNP-based Endophenotype 20932310 Caucasian ADNI 172 AD CSF P-tau181p Fluid biomarker intron_variant chr4 95815327 rs12510298 0.0000099 "PDHA2, UNC5C" NR NR NR NA PDHA2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr4 99326433 rs72681907 0.00000704 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99344800 rs283411 0.00000507 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr4 99350902 rs1662046 0.0000033 ADH1C NR NR 0.45 1.56831 ADH1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr4 99350902 rs1662046 0.0000868 ADH1C NR NR 0.55 1.73325 ADH1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr4 99350902 rs1662046 0.00511 ADH1C NR NR 0.45 1.56831 ADH1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr4 99359562 rs283404 0.00000686 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99361608 rs166892 0.00000686 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99362508 rs1229852 0.00000686 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99366025 rs283422 0.00000686 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99366839 rs283421 0.00000686 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99367818 rs283420 0.00000686 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99371030 rs283418 0.00000742 ADH1C NR NR NR NA ADH1B SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 99383266 rs284780 0.00000836 ADH1C NR NR NR NA ADH7 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr4 102267552 rs13107325 0.119 NR T T 1.073 1.073 SLC39A8 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD missense_variant chr4 102267552 rs13107325 0.141 NR T T 1.139 1.139 SLC39A8 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD missense_variant chr4 102267552 rs13107325 0.179 NR T T 1.094 1.094 SLC39A8 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD missense_variant chr4 102267552 rs13107325 0.86 NR T T 0.001 1.001 SLC39A8 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive missense_variant chr4 107052129 rs388575 0.000000015 NR C C 0.422 1.52501 DKK2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr4 107052129 rs388575 0.0014 NR C C -0.18 0.83527 DKK2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr4 107052129 rs388575 0.5 NR C C 0.05 1.05127 DKK2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr4 114132729 rs6854583 0.0000646 NR NR NR 2.13 2.13 ARSJ SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr4 114132729 rs6854583 0.00211 NR NR NR 2.38 2.38 ARSJ SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr4 114132729 rs6854583 0.00234 NR NR NR 1.78 1.78 ARSJ SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr4 114132729 rs6854583 0.0301 NR NR NR 1.59 1.59 ARSJ SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr4 119140180 rs4277762 0.0000205 MYOZ2 NR NR 1.2 1.2 MYOZ2 SNP-based Disease risk 30979435 Caucasian ADGC 6466 Age >=80 y AD AD intron_variant chr4 119140180 rs4277762 0.476 MYOZ2 NR NR 0.98 0.98 MYOZ2 SNP-based Disease risk 30979435 Caucasian ADGC 14704 Age 60-79 y AD AD intron_variant chr4 124943164 rs10022344 0.0000544 "ANKRD50, FAT4" NR NR NR NA ANKRD50 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr4 125852943 rs1911014 0.00000356 Intergenic (as reported in paper) A A NR NA FAT4 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr4 125852943 rs1911014 0.0003 NR A A NR NA FAT4 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr4 125852943 rs1911014 0.00037 NR A A NR NA FAT4 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr4 126740230 rs62324179 0.00000365 NR T T NR NA INTU SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intergenic_region chr4 137367736 rs1425967 0.0000125 NR NR NR NR NA PCDH18 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intergenic_region chr4 137367736 rs1425967 0.000039 NR NR NR NR NA PCDH18 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intergenic_region chr4 137367736 rs1425967 0.0105 NR NR NR NR NA PCDH18 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intergenic_region chr4 137405718 rs4416533 0.0000113 NR NR NR NR NA PCDH18 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intergenic_region chr4 137405718 rs4416533 0.0000361 NR NR NR NR NA PCDH18 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intergenic_region chr4 137405718 rs4416533 0.0101 NR NR NR NR NA PCDH18 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intergenic_region chr4 142704235 rs28670348 0.000181 INPP4B G G NR NA INPP4B SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr4 142704235 rs28670348 0.00101 INPP4B G G NR NA INPP4B SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intron_variant chr4 142704235 rs28670348 0.00776 INPP4B G G 1.07 1.07 INPP4B SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr4 142704235 rs28670348 0.011 INPP4B G G 1.06 1.06 INPP4B SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr4 142704235 rs28670348 0.918 INPP4B G G 1 1 INPP4B SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr4 142704235 rs28670348 0.93 INPP4B G G 0.99 0.99 INPP4B SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr4 147403157 rs13121109 0.0000064 EDNRA NR NR NR NA EDNRA SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr4 154426241 rs1466662 0.000000495 DCHS2 NR NR NR NA DCHS2 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr4 154426241 rs1466662 0.00000235 DCHS2 NR NR NR NA DCHS2 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr4 154426241 rs1466662 0.000137 DCHS2 NR NR -1 0.367879 DCHS2 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intron_variant chr4 154426241 rs1466662 0.00119 DCHS2 NR NR -0.96 0.382893 DCHS2 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intron_variant chr4 154426241 rs1466662 0.759 DCHS2 NR NR -0.58 0.559898 DCHS2 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intron_variant chr4 154733269 rs727153 0.00000337 NR C C NR NA LRAT SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 154733269 rs727153 0.00002 NR C C NR NA LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 154733269 rs727153 0.0009 Intergenic (as reported in paper) C C NR NA LRAT SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 154741179 rs12501328 0.0032 LRAT G G 1.32 1.32 LRAT SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 154741179 rs12501328 0.0266 LRAT G G 1.27 1.27 LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 154745783 rs201825 0.000000612 LRAT C C 1.3 1.3 LRAT SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 154745783 rs201825 0.00000165 LRAT C C 1.34 1.34 LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 154747558 rs201824 0.00066 LRAT T T 1.24 1.24 LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 154747733 rs201823 0.0004 LRAT G G 1.21 1.21 LRAT SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 154747733 rs201823 0.00042 LRAT G G 1.24 1.24 LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 154756163 rs156500 0.0946 LRAT C C 1.17 1.17 LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 154757193 rs156501 0.0058 LRAT A A 1.2 1.2 LRAT SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 154757193 rs156501 0.0164 LRAT A A 1.2 1.2 LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 154762064 rs149225 0.349 LRAT C C 1.06 1.06 LRAT SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 165829942 rs72635116 0.00000529 TLL1 NR NR 0.313 1.36752 TLL1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intergenic_region chr4 165829942 rs72635116 0.0000232 TLL1 NR NR 0.383 1.46668 TLL1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intergenic_region chr4 165829942 rs72635116 0.113 TLL1 NR NR 0.169 1.18412 TLL1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intergenic_region chr4 173173789 rs62341097 0.000000006 GALNT7 A A -1.15 0.316637 GALNT7 SNP-based Endophenotype 25188341 Caucasian ADGC 4046 All Neuritic Plaque Neuropathology intron_variant chr4 180964752 rs13115400 0.2 GLIS1 NR NR 0.01 1.01005 TENM3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF Ab1-42 Fluid biomarker intergenic_region chr4 180964752 rs13115400 0.24 GLIS1 NR NR 0.07 1.07251 TENM3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 704 Female AD subjects Amyloid Burden Neuropathology intergenic_region chr4 180964752 rs13115400 0.79 GLIS1 NR NR 0.02 1.0202 TENM3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 362 Male AD subjects Amyloid Burden Neuropathology intergenic_region chr4 180964752 rs13115400 3.97E-08 GLIS1 NR NR 0.03 1.03045 TENM3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF Ab1-42 Fluid biomarker intergenic_region chr4 182196767 rs13115107 0.0001 Intergenic (as reported in paper) G G NR NA TENM3 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 182196767 rs13115107 0.00032 NR G G NR NA TENM3 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr4 182196767 rs13115107 0.0005 NR G G NR NA TENM3 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr4 189068835 rs1353581 0.0000048 LINC01060 G G 0.65 0.65 FRG1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr5 458726 rs11134054 1.95E-62 EXOC3 NR NR -0.57 0.565525 EXOC3 SNP-based eQTL 22685416 Caucasian MAYO 374 All EXOC3 expression in Cerebellar Expression intron_variant chr5 458726 rs11134054 4.06E-75 EXOC3 NR NR -0.6 0.548812 EXOC3 SNP-based eQTL 22685416 Caucasian MAYO 399 All EXOC3 expression in Temporal cortex Expression intron_variant chr5 458726 rs11134054 4.77E-28 EXOC3 NR NR -0.59 0.554327 EXOC3 SNP-based eQTL 22685416 Caucasian MAYO 197 AD EXOC3 expression in Cerebellar Expression intron_variant chr5 458726 rs11134054 6.43E-30 EXOC3 NR NR -0.54 0.582748 EXOC3 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD EXOC3 expression in Cerebellar Expression intron_variant chr5 1282299 rs7725218 0.000072 TERT NR NR NR NA TERT SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intron_variant chr5 1282299 rs7725218 0.00081 TERT NR NR NR NA TERT SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intron_variant chr5 1282299 rs7725218 0.0028 TERT NR NR NR NA TERT SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intron_variant chr5 1282299 rs7725218 0.92 TERT NR NR NR NA TERT SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intron_variant chr5 7478801 rs252546 0.00000779 NR G G NR NA ADCY2 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr5 7896398 rs3776455 1.38E-129 MTRR NR NR 1.23 3.42123 MTRR SNP-based eQTL 22685416 Caucasian MAYO 399 All MTRR expression in Temporal cortex Expression intron_variant chr5 7896398 rs3776455 1.80E-64 MTRR NR NR 1.12 3.06485 MTRR SNP-based eQTL 22685416 Caucasian MAYO 197 AD MTRR expression in Cerebellar Expression intron_variant chr5 7896398 rs3776455 2.83E-127 MTRR NR NR 1.2 3.32012 MTRR SNP-based eQTL 22685416 Caucasian MAYO 374 All MTRR expression in Cerebellar Expression intron_variant chr5 7896398 rs3776455 2.97E-58 MTRR NR NR 1.3 3.6693 MTRR SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD MTRR expression in Cerebellar Expression intron_variant chr5 11107401 rs2905990 0.0000379 CTNND2 T T NR NA CTNND2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr5 11107401 rs2905990 0.00009 CTNND2 T T NR NA CTNND2 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr5 11107401 rs2905990 0.0014 CTNND2 T T NR NA CTNND2 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr5 11148581 rs757459 0.0311 CTNND2 NR NR NR NA CTNND2 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr5 14042267 rs17228994 0.000036 Intergenic (as reported in paper) C C NR NA DNAH5 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr5 14042267 rs17228994 0.0006 NR C C NR NA DNAH5 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intergenic_region chr5 14042267 rs17228994 0.0025 NR C C NR NA DNAH5 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intergenic_region chr5 15669858 rs75002042 4.70E-09 FBXL7 A A 0.6 0.6 FBXL7 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr5 15669858 rs75002042 6.19E-09 FBXL7 A A 0.61 0.61 FBXL7 SNP-based Disease risk 26339675 Caribbean Hispanic "EFIGA, NOMAS, WHICAP " 4514 All LOAD AD intron_variant chr5 29005878 rs71618613 0.00000033 SUCLG2P4 C C 0.71 0.71 CDH9 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD downstream_gene_variant chr5 29005878 rs71618613 0.0000098 SUCLG2P4 C C 0.68 0.68 CDH9 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD downstream_gene_variant chr5 29005878 rs71618613 0.0068 SUCLG2P4 C C 0.76 0.76 CDH9 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 30511 All Clinically diagnosed LOAD AD downstream_gene_variant chr5 30178906 rs13178362 0.00000066 NR C C 0.75 0.75 CDH6 SNP-based Disease risk 24755620 Caucasian ADGC 4569 All AD AD intergenic_region chr5 35080043 rs6883056 0.0000848 PRLR C C NR NA PRLR SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr5 35080043 rs6883056 0.0023 PRLR C C NR NA PRLR SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr5 35080043 rs6883056 0.471 PRLR C C 1 1 PRLR SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr5 53369400 rs35868327 0.00000026 FST A A 0.68 0.68 FST SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD intergenic_region chr5 53369400 rs35868327 0.00000078 FST A A 0.69 0.69 FST SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intergenic_region chr5 53369400 rs35868327 0.12 FST A A 0.58 0.58 FST SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 30511 All Clinically diagnosed LOAD AD intergenic_region chr5 56560548 rs3843467 0.0000025 "MAP3K1, LOC441073" NR NR NR NA MAP3K1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr5 61654384 rs11738335 0.00000428 FLJ37543 NR NR NR NA ZSWIM6 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intron_variant chr5 61654384 rs11738335 0.00000466 FLJ37543 NR NR 0.83 0.83 ZSWIM6 SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD intron_variant chr5 61654384 rs11738335 0.000572 FLJ37543 NR NR 0.75 0.75 ZSWIM6 SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD intron_variant chr5 61654384 rs11738335 0.0173 FLJ37543 NR NR 0.83 0.83 ZSWIM6 SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD intron_variant chr5 61654384 rs11738335 0.0562 FLJ37543 NR NR 0.84 0.84 ZSWIM6 SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD intron_variant chr5 61654384 rs11738335 0.0683 FLJ37543 NR NR 0.86 0.86 ZSWIM6 SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD intron_variant chr5 61654384 rs11738335 0.439 FLJ37543 NR NR 1.19 1.19 ZSWIM6 SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD intron_variant chr5 71950137 rs1217745 0.00000324 NR T T NR NA MAP1B SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD null chr5 75596177 rs5744712 0.00135 POLK C C NR NA POLK SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr5 75596177 rs5744712 0.967 POLK C C 1 1 POLK SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr5 75596177 rs5744712 1.29E-17 POLK C C NR NA POLK SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr5 75719417 rs2112347 0.108 NR T T 0.965 0.965 POC5 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD upstream_gene_variant chr5 75719417 rs2112347 0.656 NR T T 0.97 0.97 POC5 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD upstream_gene_variant chr5 75719417 rs2112347 0.675 NR T T 0 1 POC5 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive upstream_gene_variant chr5 75719417 rs2112347 0.863 NR T T 1 1 POC5 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD upstream_gene_variant chr5 77143425 rs6885904 0.0000011 "LOC728723, LOCI00129287" NR NR NR NA AC008581.2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr5 82030091 rs11741569 0.000996 ATG10 G G NR NA ATG10 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intron_variant chr5 82030091 rs11741569 9.69E-27 NR G G NR NA ATG10 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) ATG10 (ILMN_2206098) expression Expression intron_variant chr5 82066661 rs11748868 1.39E-09 NR C C NR NA ATG10 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) ATG10 expression in Putamen basal ganglia Expression intron_variant chr5 82066661 rs11748868 2.70E-09 NR C C NR NA ATG10 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) ATG10 expression in Nucleus accumbens Expression intron_variant chr5 83564666 rs67827860 1.25E-14 NR T T -0.61 0.543351 VCAN SNP-based Endophenotype 29752348 Caucasian UKBB 8239 All Fractional Anisotropy Imaging intron_variant chr5 83565581 rs13164785 3.72E-18 NR G G 0.67 1.95424 VCAN SNP-based Endophenotype 29752348 Caucasian UKBB 8239 All Mean Diffusivity Imaging intron_variant chr5 88197708 rs75451667 0.049 TMEM161B NR NR 1.51 1.51 TMEM161B SNP-based Cross phenotype 30010129 Asian Cohort from Han Chinse 475 All AD AD missense_variant chr5 88210806 rs115873146 0.0075 TMEM161B NR NR NR NA TMEM161B SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr5 88210806 rs115873146 0.43157 NA NR NR NR NA TMEM161B Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr5 88842914 rs11951031 0.0282 MEF2C A A 0.72 NA MEF2C SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr5 88885292 rs3850651 0.00028 MEF2C NR NR NR NA MEF2C SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr5 88885292 rs3850651 0.0119 NA NR NR NR NA MEF2C Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr5 88919777 rs304132 0.00000917 "MEF2C, LOC729011" NR NR NR NA MEF2C SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr5 88927603 rs190982 0.000000032 MEF2C G G 0.93 0.93 MEF2C SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr5 88927603 rs190982 0.0000025 MEF2C G G 0.92 0.92 MEF2C SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr5 88927603 rs190982 0.0000028 MEF2C G G 0.94 0.94 MEF2C SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr5 88927603 rs190982 0.00028 MEF2C G G 0.95 0.95 MEF2C SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr5 88927603 rs190982 0.0011 MEF2C G G 0.81 0.81 MEF2C SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr5 88927603 rs190982 0.0027 MEF2C G G 0.93 0.93 MEF2C SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr5 88927603 rs190982 0.0034 MEF2C G G 0.93 0.93 MEF2C SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr5 88927603 rs190982 0.00629 MEF2C G G 0.885 0.885 MEF2C SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr5 88927603 rs190982 0.0066 MEF2C G G 0.81 0.81 MEF2C SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr5 88927603 rs190982 0.66 MEF2C NR NR 0.99 0.99 MEF2C SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr5 88927603 rs190982 NR MEF2C A A 1.24 1.24 MEF2C SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr5 88927603 rs190982 NR ZCWPW1 A A 1.03 1.03 MEF2C SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr5 88927603 rs190982 NR ZCWPW1 A A 1.15 1.15 MEF2C SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr5 96987845 rs9918162 0.8 LNPEP T T 0.96 0.96 LNPEP SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr5 107836568 rs12188460 0.000623 FBXL17 G G NR NA FBXL17 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr5 107836568 rs12188460 0.000849 FBXL17 G G NR NA FBXL17 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intergenic_region chr5 107836568 rs12188460 0.00264 FBXL17 G G 1.04 1.04 FBXL17 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr5 107836568 rs12188460 0.00485 FBXL17 G G 1.04 1.04 FBXL17 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr5 107836568 rs12188460 0.25 FBXL17 G G 1.06 1.06 FBXL17 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr5 107836568 rs12188460 0.458 FBXL17 G G 1 1 FBXL17 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr5 121229828 rs919289 0.0000032 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr5 121229828 rs919289 0.000075 NR NR NR 0.56 0.56 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr5 121229828 rs919289 0.000468 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr5 121229828 rs919289 0.0105 NR NR NR 0.71 0.71 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr5 121229828 rs919289 0.09558 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr5 121229828 rs919289 0.34351 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr5 121229828 rs919289 0.744 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr5 121229828 rs919289 0.791 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr5 121229828 rs919289 1 NR NR NR 1.06 1.06 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr5 121233413 rs4895298 0.000002 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr5 121233413 rs4895298 0.000052 NR NR NR 0.55 0.55 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr5 121233413 rs4895298 0.000477 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr5 121233413 rs4895298 0.0108 NR NR NR 0.71 0.71 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr5 121233413 rs4895298 0.14639 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr5 121233413 rs4895298 0.22174 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr5 121233413 rs4895298 0.634 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr5 121233413 rs4895298 0.655 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr5 121233413 rs4895298 1 NR NR NR 1.08 1.08 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr5 121233616 rs2973413 0.00000535 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr5 121233616 rs2973413 0.000114 NR NR NR 0.56 0.56 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr5 121233616 rs2973413 0.000571 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr5 121233616 rs2973413 0.0124 NR NR NR 0.71 0.71 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr5 121233616 rs2973413 0.15152 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr5 121233616 rs2973413 0.21149 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr5 121233616 rs2973413 0.532 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr5 121233616 rs2973413 0.917 NR NR NR NR NA PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr5 121233616 rs2973413 1 NR NR NR 1.11 1.11 PRR16 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr5 121280612 rs73276571 0.0000018 NR A A 0.66 1.93479 FTMT SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr5 121280612 rs73276571 0.024 NR A A 0.22 1.24608 FTMT SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr5 121280612 rs73276571 0.13 NR A A -0.2 0.818731 FTMT SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr5 123821728 rs257016 0.00000406 AC008541.1 NR NR 0.7 0.7 CSNK1G3 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intergenic_region chr5 123821728 rs257016 0.00000541 AC008541.1 NR NR 0.71 0.71 CSNK1G3 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intergenic_region chr5 123844055 rs12514988 0.00000948 NR T T NR NA CSNK1G3 SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD intergenic_region chr5 124996410 rs4836133 0.002 NR A A 1.15 1.15 ZNF608 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intergenic_region chr5 124996410 rs4836133 0.482 NR A A 1.03 1.03 ZNF608 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intergenic_region chr5 124996410 rs4836133 0.52 NR A A 0.002 1.002 ZNF608 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intergenic_region chr5 124996410 rs4836133 0.613 NR A A 1.01 1.01 ZNF608 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intergenic_region chr5 128327887 rs39938 0.00000393 FBN2 T T 1.23 1.23 FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 15235 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr5 128327887 rs39938 0.0000143 FBN2 T T NR NA FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 15235 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr5 128327887 rs39938 0.000165 FBN2 NR NR 1.1 1.1 FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 26929 All Brain infarcts (BI) Imaging intron_variant chr5 128327887 rs39938 0.00158 FBN2 NR NR 1.1 1.1 FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 22097 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr5 128327887 rs39938 0.27 FBN2 NR NR 1.09 1.09 FBN2 SNP-based Endophenotype 30651383 Caucasian ADGC 2940 All Pathologically defined infarcts Imaging intron_variant chr5 128327887 rs39938 0.61 FBN2 NR NR 0.98 0.98 FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Brain infarcts (BI) Imaging intron_variant chr5 128327887 rs39938 0.61 FBN2 NR NR 1.01 1.01 FBN2 SNP-based Endophenotype 30651383 Caucasian "CHARGE, METASTROKE, SiGN" 137560 All Ischemic stroke (IS) Imaging intron_variant chr5 128327887 rs39938 0.88 FBN2 NR NR 1.01 1.01 FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr5 128327887 rs39938 0.9 FBN2 NR NR 1 1 FBN2 SNP-based Endophenotype 30651383 Caucasian "METASTROKE, SiGN, YLSDR" 41039 All Ischemic stroke due to small vessel disease (IS-SVD) Imaging intron_variant chr5 128327887 rs39938 1.77E-08 FBN2 T T 1.21 1.21 FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 20067 All Brain infarcts (BI) Imaging intron_variant chr5 128327887 rs39938 4.83E-08 FBN2 T T NR NA FBN2 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 20067 All Brain infarcts (BI) Imaging intron_variant chr5 131351444 rs382216 0.0000002 "ACSL6, CDC42SE2" T T 0.87 0.87 CDC42SE2 SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD intron_variant chr5 131351444 rs382216 0.0000065 "ACSL6, CDC42SE2" T T 0.88 0.88 CDC42SE2 SNP-based Disease risk 25778476 Caucasian IGAP 34152 APOE-e4- subjects AD AD intron_variant chr5 131351444 rs382216 0.002 "ACSL6, CDC42SE2" T T 0.78 0.78 CDC42SE2 SNP-based Disease risk 25778476 Caucasian ADGC 2417 APOE-e4- subjects AD AD intron_variant chr5 140289801 rs1347143 0.0000117 PFDN1 NR NR NR NA PFDN1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr5 140327854 rs11168036 0.00000032 "HBEGF, PFDN1" T T 1.12 1.12 HBEGF SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD downstream_gene_variant chr5 140327854 rs11168036 0.0000018 "HBEGF, PFDN1" T T 1.08 1.08 HBEGF SNP-based Disease risk 28183528 Multi-ethnic ADGC 33269 All AD AD downstream_gene_variant chr5 140327854 rs11168036 0.0006 "HBEGF, PFDN1" T T 1.08 1.08 HBEGF SNP-based Disease risk 28183528 Caucasian IGAP 26287 All AD AD downstream_gene_variant chr5 140327854 rs11168036 0.64 "HBEGF, PFDN1" T T 0.97 0.97 HBEGF SNP-based Disease risk 25778476 Caucasian ADGC 2417 APOE-e4- subjects AD AD downstream_gene_variant chr5 140327854 rs11168036 7.10E-09 "HBEGF, PFDN1" T T 1.08 1.08 HBEGF SNP-based Disease risk 28183528 Multi-ethnic "ADGC, IGAP" 59556 All AD AD downstream_gene_variant chr5 140327854 rs11168036 9.30E-09 "HBEGF, PFDN1" T T 1.14 1.14 HBEGF SNP-based Disease risk 25778476 Caucasian IGAP 34152 APOE-e4- subjects AD AD downstream_gene_variant chr5 140334979 rs2074613 0.000000929 HBEGF C C NR NA HBEGF SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr5 140334979 rs2074613 0.0000136 HBEGF C C NR NA HBEGF SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr5 140334979 rs2074613 0.157 HBEGF C C 1 1 HBEGF SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr5 142435923 rs4912851 0.0000232 SPRY4 G G NR NA SPRY4 SNP-based Cross phenotype 30413934 Caucasian "GIANT, UKBB" 180423 All Waist-to-hip ratio (WHR) Non-ADRD intron_variant chr5 142435923 rs4912851 0.0000339 SPRY4 G G NR NA SPRY4 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr5 142435923 rs4912851 0.00358 SPRY4 G G 1.04 1.04 SPRY4 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr5 142435923 rs4912851 0.00707 SPRY4 G G 1.04 1.04 SPRY4 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr5 142435923 rs4912851 0.232 SPRY4 G G 1.06 1.06 SPRY4 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr5 142435923 rs4912851 0.938 SPRY4 G G 1 1 SPRY4 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr5 154460912 rs6884266 0.00986 SAP30L C C NR NA SAP30L SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD 3_prime_UTR_variant chr5 154460912 rs6884266 1.72E-71 NR C C NR NA SAP30L SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group SAP30L (ILMN_1843932) expression Expression 3_prime_UTR_variant chr5 157762610 rs11738432 1.68E-33 THG1L NR NR -0.81 0.444858 LSM11 SNP-based eQTL 22685416 Caucasian MAYO 197 AD THG1L expression in Cerebellar Expression downstream_gene_variant chr5 157762610 rs11738432 2.45E-39 THG1L NR NR -0.94 0.390628 LSM11 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD THG1L expression in Cerebellar Expression downstream_gene_variant chr5 157762610 rs11738432 3.12E-97 THG1L NR NR -1.09 0.336216 LSM11 SNP-based eQTL 22685416 Caucasian MAYO 399 All THG1L expression in Temporal cortex Expression downstream_gene_variant chr5 157762610 rs11738432 3.58E-78 THG1L NR NR -0.86 0.423162 LSM11 SNP-based eQTL 22685416 Caucasian MAYO 374 All THG1L expression in Cerebellar Expression downstream_gene_variant chr5 160961636 rs2176298 0.00015 LOC285629 T T NR NA ATP10B SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr5 160961636 rs2176298 0.000456 LOC285629 T T NR NA ATP10B SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total triglycerides (TG) Non-ADRD intergenic_region chr5 160961636 rs2176298 0.0147 LOC285629 T T 1.03 1.03 ATP10B SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr5 160961636 rs2176298 0.0307 LOC285629 T T 1.03 1.03 ATP10B SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr5 160961636 rs2176298 0.186 LOC285629 T T 1 1 ATP10B SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr5 160961636 rs2176298 0.452 LOC285629 T T 0.96 0.96 ATP10B SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr5 168466703 rs12514426 0.000928 WWC1 NR NR NR NA WWC1 SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intron_variant chr5 168466703 rs12514426 0.00498 WWC1 NR NR NR NA WWC1 SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intron_variant chr5 168466703 rs12514426 0.0359 WWC1 NR NR NR NA WWC1 SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intron_variant chr5 171439292 rs62383992 0.000912 FGF18 A A NR NA FGF18 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr5 171439292 rs62383992 0.0013 FGF18 A A NR NA FGF18 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr5 171439292 rs62383992 0.15 FGF18 A A 1 1 FGF18 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr5 174587111 rs145848414 0.000000069 NR A A 2.29 2.29 MSX2 SNP-based Disease risk 23571587 African American ADGC 5896 All LOAD AD intergenic_region chr5 178148265 rs3812071 0.0223 RMND5B C C NR NA RMND5B SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD 3_prime_UTR_variant chr5 178148265 rs3812071 8.86E-14 NR C C NR NA RMND5B SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group RMND5B (ILMN_1737847) expression Expression 3_prime_UTR_variant chr5 180394728 rs11249708 0.000015 GFPT2 NR NR NR NA GFPT2 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intergenic_region chr5 180394728 rs11249708 0.00012 GFPT2 NR NR NR NA GFPT2 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intergenic_region chr5 180394728 rs11249708 0.0006 GFPT2 NR NR NR NA GFPT2 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intergenic_region chr5 180394728 rs11249708 0.13 GFPT2 NR NR NR NA GFPT2 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intergenic_region chr6 2838014 rs316341 0.00462 GLIS1 G G 0.04 1.04081 SERPINB1 SNP-based Age at onset (AAO) / Survival 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 39855 AD subjects Age at onset Other intron_variant chr6 2838014 rs316341 0.009 GLIS1 NR NR 0.02 1.0202 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF Ab1-42 Fluid biomarker intron_variant chr6 2838014 rs316341 0.00919 GLIS1 G G 0.02 1.0202 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF T-tau Fluid biomarker intron_variant chr6 2838014 rs316341 0.06 GLIS1 NR NR 0.19 1.20925 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 362 Male AD subjects Amyloid Burden Neuropathology intron_variant chr6 2838014 rs316341 0.152 GLIS1 G G 1.03 2.80107 SERPINB1 SNP-based Disease risk 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 74046 All AD risk AD intron_variant chr6 2838014 rs316341 0.22 GLIS1 G G 0.01 1.01005 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF P-tau181p Fluid biomarker intron_variant chr6 2838014 rs316341 0.277 GLIS1 G G 0.05 1.05127 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1530 All AD Progression (based on CDR Score) Cognitive intron_variant chr6 2838014 rs316341 0.99 GLIS1 NR NR 0.001 1.001 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 704 Female AD subjects Amyloid Burden Neuropathology intron_variant chr6 2838014 rs316341 1.72E-08 GLIS1 NR NR 0.025 1.02532 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF Ab1-42 Fluid biomarker intron_variant chr6 2838014 rs316341 1.76E-08 GLIS1 G G 0.025 1.02532 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF Ab1-42 Fluid biomarker intron_variant chr6 2838014 rs316341 4.25E-08 GLIS1 NR NR 0.03 1.03045 SERPINB1 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF Ab1-42 Fluid biomarker intron_variant chr6 3979517 rs9392025 0.00276 HLA-DRB1 A A 0.83 NA PRPF4B SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other upstream_gene_variant chr6 7281421 rs1050226 0.0000027 "RREB1, SSR1" NR NR NR NA SSR1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD 3_prime_UTR_variant chr6 11334421 rs760678 0.852 NEDD9 C C 0.99 0.99 NEDD9 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr6 19350484 rs62402815 0.000000429 LOC101928519 G G 0.61 0.61 ID4 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD downstream_gene_variant chr6 19350484 rs62402815 0.0000018 LOC101928519 G G 0.69 0.69 ID4 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD downstream_gene_variant chr6 20541966 rs10484634 0.00000097 CDKAL1 NR NR NR NA CDKAL1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr6 20578621 rs13205786 0.0000012 CDKAL1 NR NR NR NA CDKAL1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr6 20612985 rs13200415 0.00000078 CDKAL1 NR NR NR NA CDKAL1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr6 20675064 rs1012635 0.0000004 CDKAL1 NR NR NR NA CDKAL1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr6 20717173 rs10946403 9.00E-20 CDKAL1 NR NR NR NA CDKAL1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr6 20731293 rs7741604 0.000000086 CDKAL1 NR NR NR NA CDKAL1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr6 20762940 rs4712540 0.0000058 CDKAL1 NR NR NR NA CDKAL1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr6 23378723 rs1925458 0.00000126 NRSN1 G G 0.64 0.64 NRSN1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 10870 HTN-P group AD AD intergenic_region chr6 26114144 rs198834 2.11E-61 HIST1H4C NR NR -0.43 0.650509 H2BC4 SNP-based eQTL 22685416 Caucasian MAYO 374 All HIST1H4C expression in Cerebellar Expression downstream_gene_variant chr6 26114144 rs198834 3.35E-48 HIST1H4C NR NR -0.52 0.594521 H2BC4 SNP-based eQTL 22685416 Caucasian MAYO 399 All HIST1H4C expression in Temporal cortex Expression downstream_gene_variant chr6 26114144 rs198834 3.92E-32 HIST1H4C NR NR -0.44 0.644036 H2BC4 SNP-based eQTL 22685416 Caucasian MAYO 197 AD HIST1H4C expression in Cerebellar Expression downstream_gene_variant chr6 26114144 rs198834 8.78E-24 HIST1H4C NR NR -0.42 0.657047 H2BC4 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD HIST1H4C expression in Cerebellar Expression downstream_gene_variant chr6 27123646 rs6913660 0.54 HIST1H2BJ NR NR 1.04 1.04 H2BC11 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD upstream_gene_variant chr6 27123646 rs6913660 0.95 HIST1H2BJ NR NR 1.01 1.01 H2BC11 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD upstream_gene_variant chr6 27176104 rs13194053 0.5 MHC NR NR 0.96 0.96 H2AC12 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intergenic_region chr6 27281152 rs6932590 0.33 PRSS16 NR NR 0.88 0.88 POM121L2 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD downstream_gene_variant chr6 27281152 rs6932590 0.58 PRSS16 NR NR 0.97 0.97 POM121L2 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD downstream_gene_variant chr6 28209714 rs988084 3.28E-09 "TOB2P1, ZNF192P1" NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker intergenic_region chr6 28209714 rs988084 7.01E-26 "TOB2P1, ZNF192P1" NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker intergenic_region chr6 28209810 rs988083 3.28E-09 "TOB2P1, ZNF192P1" NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker intergenic_region chr6 28209810 rs988083 7.01E-26 "TOB2P1, ZNF192P1" NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker intergenic_region chr6 28216108 rs1150701 1.18E-08 TOB2P1 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker downstream_gene_variant chr6 28216108 rs1150701 1.44E-26 TOB2P1 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker downstream_gene_variant chr6 28216319 rs1150702 1.18E-08 TOB2P1 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker downstream_gene_variant chr6 28216319 rs1150702 1.44E-26 TOB2P1 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker downstream_gene_variant chr6 28216482 rs1150703 3.28E-09 TOB2P1 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker downstream_gene_variant chr6 28216482 rs1150703 7.01E-26 TOB2P1 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker downstream_gene_variant chr6 28225353 rs1233712 1.18E-08 ZSCAN9 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker 5_prime_UTR_variant chr6 28225353 rs1233712 1.44E-26 ZSCAN9 NR NR NR NA ZSCAN9 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker 5_prime_UTR_variant chr6 28289600 rs13211507 0.79 PGBD1 NR NR 0.94 0.94 PGBD1 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr6 28289600 rs13211507 0.95 PGBD1 NR NR 1.01 1.01 PGBD1 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr6 28296904 rs3800324 0.00032 PGBD1 NR NR 1.43 1.43 PGBD1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD missense_variant chr6 28296904 rs3800324 0.026 PGBD1 NR NR NR NA PGBD1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD missense_variant chr6 28296904 rs3800324 0.146 PGBD1 NR NR NR NA PGBD1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD missense_variant chr6 28296904 rs3800324 0.159 PGBD1 A A 1.3 1.3 PGBD1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD missense_variant chr6 28296904 rs3800324 0.204 PGBD1 NR NR NR NA PGBD1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD missense_variant chr6 28296904 rs3800324 0.317 PGBD1 NR NR NR NA PGBD1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD missense_variant chr6 28296904 rs3800324 0.502 PGBD1 NR NR NR NA PGBD1 SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD missense_variant chr6 28363475 rs213228 0.018 ZKSCAN3 NR NR NR NA ZKSCAN3 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 28390543 rs1361385 0.0098 ZSCAN12 NR NR NR NA ZSCAN12 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 29555869 rs444013 0.00079 UBD NR NR 1.11 1.11 OR2I1P SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD 3_prime_UTR_variant chr6 29555869 rs444013 0.01 UBD NR NR NR NA OR2I1P SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD 3_prime_UTR_variant chr6 29555869 rs444013 0.042 UBD NR NR NR NA OR2I1P SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD 3_prime_UTR_variant chr6 29555869 rs444013 0.299 UBD NR NR NR NA OR2I1P SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD 3_prime_UTR_variant chr6 29555869 rs444013 0.741 UBD NR NR NR NA OR2I1P SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD 3_prime_UTR_variant chr6 29555869 rs444013 0.845 UBD NR NR NR NA OR2I1P SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD 3_prime_UTR_variant chr6 29854484 rs2975033 1.57E-78 HLA-H NR NR 1.45 4.26311 HLA-G SNP-based eQTL 22685416 Caucasian MAYO 374 All HLA-H expression in Cerebellar Expression upstream_gene_variant chr6 29854484 rs2975033 3.61E-36 HLA-H NR NR 1.39 4.01485 HLA-G SNP-based eQTL 22685416 Caucasian MAYO 197 AD HLA-H expression in Cerebellar Expression upstream_gene_variant chr6 29854484 rs2975033 3.63E-36 HLA-H NR NR 1.53 4.61818 HLA-G SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD HLA-H expression in Cerebellar Expression upstream_gene_variant chr6 30066107 rs3807031 0.0000116 PPP1R11 NR NR NR NA PPP1R11 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD upstream_gene_variant chr6 30171922 rs929156 0.0000169 TRIM15 NR NR NR NA TRIM15 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD missense_variant chr6 31114212 rs3130977 0.0349 C6orf15 NR NR NR NA PSORS1C1 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging upstream_gene_variant chr6 31146405 rs746647 0.0496 CCHCR1 NR NR NR NA CCHCR1 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 31844261 rs9267576 0.000017 "C6orf48, NEU1" NR NR NR NA NEU1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD downstream_gene_variant chr6 31871532 rs2242665 0.0254 SLC44A4 NR NR NR NA SLC44A4 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging missense_variant chr6 31876147 rs2736428 0.0246 SLC44A4 NR NR NR NA SLC44A4 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 31893364 rs2844457 0.0116 EHMT2 NR NR NR NA EHMT2 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 31926167 rs2734335 0.0445 C2 NR NR NR NA C2 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 31949763 rs4151657 0.0307 CFB NR NR NR NA AL645922.1 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 31962664 rs592229 0.0078 SKIV2L NR NR NR NA SKIV2L SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 32053353 rs11969759 0.0000021 TNXB C C 0.62 0.62 TNXB SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr6 32056618 rs10947230 0.00000233 TNXB C C 0.62 0.62 TNXB SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD missense_variant chr6 32062507 rs2239689 0.0088 TNXB NR NR NR NA TNXB SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 32078498 rs7774197 0.00000417 TNXB A A 0.63 0.63 TNXB SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr6 32121077 rs2228628 0.0316 ATF6B NR NR NR NA ATF6B SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging synonymous_variant chr6 32205216 rs3131296 0.15 NOTCH4 NR NR 1.16 1.16 NOTCH4 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr6 32205216 rs3131296 0.33 NOTCH4 NR NR 1.07 1.07 NOTCH4 SNP-based Cross phenotype 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 6958 AD+P and control subjects AD+Psychosis ADRD intron_variant chr6 32323177 rs485774 0.0331 C6orf10 NR NR NR NA TSBP1 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr6 32463370 rs9268877 0.000031 HLA-DRA A A NR NA HLA-DRA SNP-based eQTL 27899424 Caucasian UKBEC 101 All HLA-DPA1 expression in Frontal cortex Expression intron_variant chr6 32463370 rs9268877 1.04E-10 HLA-DRA NR NR NR NA HLA-DRA SNP-based Disease risk 27899424 Caucasian IFGC 12928 All Frontotemporal Dementia ADRD intron_variant chr6 32539133 rs116715716 0.0000225 HLA-DRB1 T T NR NA HLA-DRB5 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intergenic_region chr6 32539133 rs116715716 0.0000787 HLA-DRB1 T T NR NA HLA-DRB5 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr6 32542705 rs115124923 3.98E-08 HLA-DRB5 NR NR 0.17 NA HLA-DRB5 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intergenic_region chr6 32582545 rs9269853 2.66E-08 HLA-DRB1 T T NR NA HLA-DRB1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr6 32602623 rs2516049 0.0000361 HLA-DRB5 NR NR NR NA HLA-DRB1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr6 32602623 rs2516049 0.0000537 HLA-DRB5 T T NR NA HLA-DRB1 SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD intergenic_region chr6 32602623 rs2516049 6.03E-15 HLA-DRB5 T T NR NA HLA-DRB1 SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 7484 All Psoriasis Non-ADRD intergenic_region chr6 32607629 rs9271058 0.000000051 HLA-DRB1 A A 1.1 1.1 HLA-DRB1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intergenic_region chr6 32607629 rs9271058 0.000057 HLA-DRB1 A A 1.11 1.11 HLA-DRB1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intergenic_region chr6 32607629 rs9271058 1.40E-11 HLA-DRB1 A A 1.1 1.1 HLA-DRB1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intergenic_region chr6 32609720 rs536810 0.00000718 HLA-DRB5 T T NR NA HLA-DQA1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr6 32609720 rs536810 0.000203 HLA-DRB5 T T 0.99 0.99 HLA-DQA1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr6 32609720 rs536810 0.153 HLA-DRB5 T T 0.93 0.93 HLA-DQA1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr6 32609720 rs536810 1.14E-08 HLA-DRB5 T T 0.92 0.92 HLA-DQA1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr6 32609720 rs536810 3.48E-08 HLA-DRB5 T T 0.92 0.92 HLA-DQA1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr6 32609720 rs536810 4.33E-14 HLA-DRB5 T T NR NA HLA-DQA1 SNP-based Cross phenotype 30413934 Caucasian "GIANT, UKBB" 180423 All Waist-to-hip ratio (WHR) Non-ADRD intergenic_region chr6 32610753 rs9271192 0.000000016 "HLA-DRB1, HLA-DRB5" C C 1.11 1.11 HLA-DQA1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intergenic_region chr6 32610753 rs9271192 0.000042 "HLA-DRB1, HLA-DRB5" C C 1.12 1.12 HLA-DQA1 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intergenic_region chr6 32610753 rs9271192 0.000266 HLA-DRB5 NR NR 1.11 1.11 HLA-DQA1 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD intergenic_region chr6 32610753 rs9271192 0.34 "HLA-DRB, HLA-DRB5" C C 1.08 1.08 HLA-DQA1 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intergenic_region chr6 32610753 rs9271192 0.59 "HLA-DRB, HLA-DRB5" C C 1.04 1.04 HLA-DQA1 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intergenic_region chr6 32610753 rs9271192 2.90E-12 "HLA-DRB1, HLA-DRB5" C C 1.11 1.11 HLA-DQA1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intergenic_region chr6 32610753 rs9271192 NR "HLA-DRB1, HLA-DRB5" C C 1.01 1.01 HLA-DQA1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intergenic_region chr6 32610753 rs9271192 NR ZCWPW1 C C 0.93 0.93 HLA-DQA1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intergenic_region chr6 32610753 rs9271192 NR ZCWPW1 C C 1.03 1.03 HLA-DQA1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intergenic_region chr6 32615580 rs6931277 0.000000178 HLA-DRB1 T T NR NA HLA-DQA1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intergenic_region chr6 32615580 rs6931277 8.41E-11 HLA-DRB1 T T -6.49 NA HLA-DQA1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intergenic_region chr6 32638163 rs1318392492 0.132 HLA-DRB5 G G 0.86 NA SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other NA chr6 32639364 rs9272561 0.000000723 HLA-DQA1 G G NR NA HLA-DQA1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD 3_prime_UTR_variant chr6 32639364 rs9272561 5.37E-09 HLA-DQA1 G G NR NA HLA-DQA1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr6 32702056 rs115675626 0.000631 HLA-DQB1 NR NR -0.11 NA HLA-DQB1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other downstream_gene_variant chr6 32715085 rs3892710 0.00000232 HLA-DQA2 T T -0.2 0.818731 HLA-DQA2 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology upstream_gene_variant chr6 33857581 rs2104362 0.00000503 "LEMD2, MLN, MIR1275" NR NR NR NA MLN SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intergenic_region chr6 33857581 rs2104362 0.00000691 "LEMD2, MLN, MIR1275" NR NR NR NA MLN SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intergenic_region chr6 33857581 rs2104362 0.000836 "LEMD2, MLN, MIR1275" NR NR 0.9 2.4596 MLN SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intergenic_region chr6 33857581 rs2104362 0.00587 "LEMD2, MLN, MIR1275" NR NR 0.84 2.31637 MLN SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intergenic_region chr6 33857581 rs2104362 0.0679 "LEMD2, MLN, MIR1275" NR NR 4.4 81.4509 MLN SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intergenic_region chr6 34335092 rs206936 0.318 NR G G 0.956 0.956 NUDT3 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr6 34335092 rs206936 0.365 NR G G 0.976 0.976 NUDT3 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr6 34335092 rs206936 0.756 NR G G 0 1 NUDT3 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr6 34335092 rs206936 0.83 NR G G 0.99 0.99 NUDT3 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr6 40833992 rs12664598 0.00000652 NR G G NR NA UNC5CL SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intergenic_region chr6 40842273 rs9369240 0.00000487 NR G G NR NA UNC5CL SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intergenic_region chr6 40974457 rs187370608 1.45E-16 TREM2 A A 8.26 NA UNC5CL SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intergenic_region chr6 41066261 rs114812713 0.0072 OARD1 C C 1.23 1.23 OARD1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 30511 All Clinically diagnosed LOAD AD 3_prime_UTR_variant chr6 41066261 rs114812713 2.10E-13 OARD1 C C 1.32 1.32 OARD1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD 3_prime_UTR_variant chr6 41066261 rs114812713 4.50E-12 OARD1 C C 1.35 1.35 OARD1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD 3_prime_UTR_variant chr6 41158917 rs2234256 0.56 TREM2 G G 0 0 SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 784 All AD AD NA chr6 41159805 rs2234255 0.36 TREM2 A A NA NA SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 785 All AD AD NA chr6 41159867 rs149622783 1 TREM2 T T 1.8 1.8 SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 782 All AD AD NA chr6 41161362 rs147564421 0.5 TREM2 A A NA NA SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 2198 All AD AD NA chr6 41161367 rs2234253 0.72 TREM2 T T 1.4 1.4 SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 2196 All AD AD NA chr6 41161395 rs142232675 0.02 TREM2 T T NA NA SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 2196 All AD AD NA chr6 41161457 rs201258663 0.5 TREM2 A A NA NA SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 2198 All AD AD NA chr6 41161469 rs143332484 0.000000366 TREM2 T T 3.97 3.97 TREM2 SNP-based Disease risk 28714976 Caucasian "CHARGE, EADI, GERAD" 3968 All AD AD missense_variant chr6 41161469 rs143332484 0.00245 TREM2 T T 1.55 1.55 TREM2 SNP-based Disease risk 28714976 Caucasian ADGC 15288 All AD AD missense_variant chr6 41161469 rs143332484 0.5 TREM2 T T 0.8 0.8 TREM2 SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 2194 All AD AD missense_variant chr6 41161469 rs143332484 1.55E-14 TREM2 T T 1.67 1.67 TREM2 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 53042 All AD AD missense_variant chr6 41161469 rs143332484 3.48E-09 TREM2 T T 1.58 1.58 TREM2 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 33786 All AD AD missense_variant chr6 41161514 rs75932628 0.00000123 TREM2 T T 2.58 2.58 TREM2 SNP-based Disease risk 28714976 Caucasian ADGC 14884 All AD AD missense_variant chr6 41161514 rs75932628 0.00000739 TREM2 NR NR 4.66 4.66 TREM2 SNP-based Disease risk 23150908 Caucasian Cohort from Europe 4786 All AD AD missense_variant chr6 41161514 rs75932628 0.00015 TREM2 T T 2.5 2.5 TREM2 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD missense_variant chr6 41161514 rs75932628 0.00053 TREM2 NR NR 0.19 1.20925 TREM2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker missense_variant chr6 41161514 rs75932628 0.00069 TREM2 NR NR 0.19 1.20925 TREM2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker missense_variant chr6 41161514 rs75932628 0.0013 TREM2 NR NR 0.18 1.19722 TREM2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker missense_variant chr6 41161514 rs75932628 0.002 TREM2 NR NR 0.16 1.17351 TREM2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker missense_variant chr6 41161514 rs75932628 0.002 TREM2 NR NR 2.83 2.83 TREM2 SNP-based Disease risk 23150908 Caucasian "ADGC, Cohort from Europe" 11764 All AD AD missense_variant chr6 41161514 rs75932628 0.0026 TREM2 NR NR 0.16 1.17351 TREM2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker missense_variant chr6 41161514 rs75932628 0.0047 TREM2 NR NR 0.15 1.16183 TREM2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker missense_variant chr6 41161514 rs75932628 0.04 TREM2 NR NR 3.15 3.15 TREM2 SNP-based Disease risk 23150908 Caucasian Cohort from Europe 2408 All AD AD missense_variant chr6 41161514 rs75932628 0.07 TREM2 NR NR 2.45 2.45 TREM2 SNP-based Disease risk 23150908 Caucasian Cohort from Europe 5894 All AD AD missense_variant chr6 41161514 rs75932628 0.14 TREM2 NR NR 3.52 3.52 TREM2 SNP-based Disease risk 23150908 Caucasian Cohort from Europe 2661 All AD AD missense_variant chr6 41161514 rs75932628 0.37 TREM2 NR NR 3.03 3.03 TREM2 SNP-based Disease risk 23150908 Caucasian ADGC 801 All AD AD missense_variant chr6 41161514 rs75932628 1.13E-08 TREM2 NR NR 2.62 2.62 TREM2 SNP-based Disease risk 23150908 Caucasian Cohort from Europe 113600 All AD AD missense_variant chr6 41161514 rs75932628 2.70E-15 TREM2 T T 2.08 2.08 TREM2 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD missense_variant chr6 41161514 rs75932628 2.90E-12 TREM2 T T 2.01 2.01 TREM2 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD missense_variant chr6 41161514 rs75932628 3.02E-12 TREM2 T T 2.46 2.46 TREM2 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 30018 All AD AD missense_variant chr6 41161514 rs75932628 3.42E-10 TREM2 NR NR 2.92 2.92 TREM2 SNP-based Disease risk 23150908 Caucasian Cohort from Europe 12438 All AD AD missense_variant chr6 41161514 rs75932628 4.38E-08 TREM2 T T 2.37 2.37 TREM2 SNP-based Disease risk 28714976 Caucasian "CHARGE, EADI, GERAD" 35831 All AD AD missense_variant chr6 41161514 rs75932628 5.38E-24 TREM2 T T 2.46 2.46 TREM2 SNP-based Disease risk 28714976 Caucasian "ADGC, CHARGE, EADI, GERAD" 80733 All AD AD missense_variant chr6 41161514 rs75932628 <1.00E-03 TREM2 T T 4.5 4.5 TREM2 SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 2196 All AD AD missense_variant chr6 41161557 rs104894002 0.25 TREM2 A A NA NA SNP-based Disease risk 23150934 Caucasian "Cohorts from Europe, USA" 2187 All AD AD NA chr6 41170311 rs12202176 0.484 TREM2 A A 1.19 NA TREM2 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intergenic_region chr6 41186912 rs9381040 0.845 TREML2 T T 0.991 0.991 TREML2 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD downstream_gene_variant chr6 41197050 rs6916710 0.0064 NR NR NR -0.03 0.970446 TREML2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker intron_variant chr6 41197050 rs6916710 0.007 NR NR NR -0.03 0.970446 TREML2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker intron_variant chr6 41197050 rs6916710 0.0082 NR NR NR -0.03 0.970446 TREML2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker intron_variant chr6 41197050 rs6916710 0.0093 NR NR NR -0.03 0.970446 TREML2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker intron_variant chr6 41197050 rs6916710 0.011 NR NR NR -0.03 0.970446 TREML2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker intron_variant chr6 41197050 rs6916710 0.015 NR NR NR -0.03 0.970446 TREML2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker intron_variant chr6 41368363 rs6922617 0.000000349 NR NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.00000166 NR NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.00000234 NR NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.0000049 NR NR NR -0.1 0.904837 NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.0000061 NR NR NR -0.1 0.904837 NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.0000065 NR NR NR -0.1 0.904837 NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF P-tau181p Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.0000255 NCR2 NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.000032 NR NR NR -0.1 0.904837 NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.000041 NR NR NR -0.1 0.904837 NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.000046 NR NR NR -0.1 0.904837 NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC" 815 All CSF T-tau Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.0000461 NR NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.000122 NR NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.000403 NR NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.00369 NCR2 NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intergenic_region chr6 41368363 rs6922617 0.33 NR A A 0.007 1.00702 NCR2 SNP-based Cognitive 23562540 NR ROSMAP 1593 All global cognitive decline Cognitive intergenic_region chr6 41368363 rs6922617 0.547 NR A A -0.029 0.971416 NCR2 SNP-based Neuropathology 23562540 NR ROSMAP 651 All tangle counts Neuropathology intergenic_region chr6 41368363 rs6922617 0.677 NR A A -0.0174 0.982751 NCR2 SNP-based Disease risk 23562540 Caucasian ADGC 22771 All AD AD intergenic_region chr6 41368363 rs6922617 3.58E-08 NCR2 NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr6 41372834 rs11966476 0.0000159 NCR2 NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intergenic_region chr6 41372834 rs11966476 0.00399 NCR2 NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intergenic_region chr6 41372834 rs11966476 4.97E-08 NCR2 NR NR NR NA NCR2 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intergenic_region chr6 42972935 rs2395943 1.61E-70 PEX6 NR NR -0.39 0.677057 PEX6 SNP-based eQTL 22685416 Caucasian MAYO 374 All PEX6 expression in Cerebellar Expression intron_variant chr6 42972935 rs2395943 3.13E-29 PEX6 NR NR -0.39 0.677057 PEX6 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD PEX6 expression in Cerebellar Expression intron_variant chr6 42972935 rs2395943 4.40E-66 PEX6 NR NR -0.46 0.631284 PEX6 SNP-based eQTL 22685416 Caucasian MAYO 399 All PEX6 expression in Temporal cortex Expression intron_variant chr6 42972935 rs2395943 8.43E-36 PEX6 NR NR -0.4 0.67032 PEX6 SNP-based eQTL 22685416 Caucasian MAYO 197 AD PEX6 expression in Cerebellar Expression intron_variant chr6 43560704 rs1096699 2.70E-50 MAD2L1BP NR NR 1.31 3.70617 POLR1C SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD MAD2L1BP expression in Cerebellar Expression intron_variant chr6 43560704 rs1096699 2.90E-54 MAD2L1BP NR NR 1.22 3.38719 POLR1C SNP-based eQTL 22685416 Caucasian MAYO 197 AD MAD2L1BP expression in Cerebellar Expression intron_variant chr6 43560704 rs1096699 6.25E-111 MAD2L1BP NR NR 1.26 3.52542 POLR1C SNP-based eQTL 22685416 Caucasian MAYO 374 All MAD2L1BP expression in Cerebellar Expression intron_variant chr6 46217747 rs4530856 0.0000127 RCAN2 NR NR NR NA RCAN2 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD downstream_gene_variant chr6 47430010 rs2184397 0.00000551 "CD2AP, TNFRSF21" NR NR NR NA CD2AP SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr6 47463548 rs9473117 0.00000023 CD2AP C C 1.09 1.09 CD2AP SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD upstream_gene_variant chr6 47463548 rs9473117 0.0001 CD2AP C C 1.11 1.11 CD2AP SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD upstream_gene_variant chr6 47463548 rs9473117 1.20E-10 CD2AP C C 1.09 1.09 CD2AP SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD upstream_gene_variant chr6 47464901 rs9381563 0.0000081 CD2AP C C NR NA CD2AP SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD upstream_gene_variant chr6 47464901 rs9381563 2.52E-10 CD2AP C C 6.33 NA CD2AP SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD upstream_gene_variant chr6 47464901 rs9381563 5.35E-09 CD2AP C C NR NA CD2AP SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD upstream_gene_variant chr6 47484534 rs9296559 0.0015 CD2AP NR NR 1.1 1.1 CD2AP SNP-based Disease risk 21460840 Caucasian "EADI, GERAD" 13448 All AD AD intron_variant chr6 47485642 rs9349407 0.00000103 CD2AP C C 1.12 1.12 CD2AP SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr6 47485642 rs9349407 0.00000117 CD2AP C C 1.14 1.14 CD2AP SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr6 47485642 rs9349407 0.00000205 CD2AP C C 1.12 1.12 CD2AP SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr6 47485642 rs9349407 0.00000529 CD2AP C C 1.14 1.14 CD2AP SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr6 47485642 rs9349407 0.0008 CD2AP NR NR 1.11 1.11 CD2AP SNP-based Disease risk 21460840 Caucasian "EADI, GERAD" 13448 All AD AD intron_variant chr6 47485642 rs9349407 0.002 CD2AP NR NR 1.09 1.09 CD2AP SNP-based Disease risk 21460841 Caucasian "CHARGE, EADI, GERAD" 25818 All LOAD AD intron_variant chr6 47485642 rs9349407 0.029 NR C C 0.07 1.07251 CD2AP SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology intron_variant chr6 47485642 rs9349407 0.0738 CD2AP C C 1.08 1.08 CD2AP SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr6 47485642 rs9349407 0.118 CD2AP C C 1.07 1.07 CD2AP SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr6 47485642 rs9349407 0.273 CD2AP C C -0.14 0.869358 CD2AP SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr6 47485642 rs9349407 0.383 CD2AP G G 0.94 0.94 CD2AP SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr6 47485642 rs9349407 0.765 CD2AP C C -0.03 0.970446 CD2AP SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr6 47485642 rs9349407 0.854 CD2AP C C 0.98 0.98 CD2AP SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr6 47485642 rs9349407 8.60E-09 CD2AP NR NR 1.11 1.11 CD2AP SNP-based Disease risk 21460840 Caucasian "ADGC, GERAD" NR All AD AD intron_variant chr6 47485642 rs9349407 8.60E-09 CD2AP NR NR 1.11 1.11 CD2AP SNP-based Disease risk 21460841 Caucasian "ADGC, CHARGE, EADI, GERAD" 48589 All LOAD AD intron_variant chr6 47520026 rs10948363 0.000000031 CD2AP G G 1.1 1.1 CD2AP SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr6 47520026 rs10948363 0.0000164 CD2AP NR NR 0.343 1.40917 CD2AP SNP-based eQTL 30448613 Caucasian UKBEC 49 All AK9 (t2969159) expression in frontal cortex Expression intron_variant chr6 47520026 rs10948363 0.00041 CD2AP G G 1.09 1.09 CD2AP SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr6 47520026 rs10948363 0.16 CD2AP G G 1.1 1.1 CD2AP SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr6 47520026 rs10948363 0.38 CD2AP G G 1.08 1.08 CD2AP SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr6 47520026 rs10948363 0.67 CD2AP NR NR 0.97 0.97 CD2AP SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr6 47520026 rs10948363 5.20E-11 CD2AP G G 1.1 1.1 CD2AP SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr6 47520026 rs10948363 NR CD2AP G G 0.73 0.73 CD2AP SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr6 47520026 rs10948363 NR ZCWPW1 G G 0.35 0.35 CD2AP SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr6 47520026 rs10948363 NR ZCWPW1 G G 0.99 0.99 CD2AP SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr6 47581893 rs3818866 0.23 CD2AP C C 1.09 NA CD2AP SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr6 47710446 rs1109581 0.00251 GPR115 NR NR -0.07 NA ADGRF4 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr6 50835337 rs987237 0.268 NR G G 0.95 0.95 TFAP2B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr6 50835337 rs987237 0.542 NR G G 1.03 1.03 TFAP2B SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr6 50835337 rs987237 0.553 NR G G 0 1 TFAP2B SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr6 50835337 rs987237 0.679 NR G G 0.988 0.988 TFAP2B SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr6 52792754 rs4715326 1.18E-08 GSTA1 NR NR -0.14 0.869358 GSTA1 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma GST-alpha Fluid biomarker intron_variant chr6 53390978 rs12194027 0.000139 ELOVL5 C C NR NA ELOVL5 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr6 53390978 rs12194027 0.000153 ELOVL5 C C NR NA ELOVL5 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total triglycerides (TG) Non-ADRD intergenic_region chr6 53390978 rs12194027 0.147 ELOVL5 C C 1 1 ELOVL5 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr6 56433924 rs12195424 0.00000287 DST NR NR 0.35 1.41907 DST SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker upstream_gene_variant chr6 56433924 rs12195424 0.000407 DST NR NR 0.338 1.40214 DST SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker upstream_gene_variant chr6 56433924 rs12195424 0.00611 DST NR NR 0.336 1.39934 DST SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker upstream_gene_variant chr6 56439165 rs77121579 0.00000369 DST NR NR 0.384 1.46815 DST SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intergenic_region chr6 56439165 rs77121579 0.000269 DST NR NR 0.383 1.46668 DST SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intergenic_region chr6 56439165 rs77121579 0.0168 DST NR NR 0.333 1.39515 DST SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intergenic_region chr6 57434294 rs2191651 1.36E-53 PRIM2 NR NR -0.57 0.565525 PRIM2 SNP-based eQTL 22685416 Caucasian MAYO 399 All PRIM2 expression in Temporal cortex Expression intron_variant chr6 60650744 rs7774782 0.000183 PRIM2 C C NR NA PRIM2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intergenic_region chr6 60650744 rs7774782 0.000293 PRIM2 C C NR NA PRIM2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr6 60650744 rs7774782 0.506 PRIM2 C C 1 1 PRIM2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr6 62352030 rs12527308 0.31 NR T T 0.09 1.09417 KHDRBS2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF Ab1-42 Fluid biomarker intergenic_region chr6 67011595 rs12203791 0.000000976 NR T T NR NA EYS SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr6 68905723 rs10485435 0.000000614 NR T T NR NA ADGRB3 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr6 69884522 rs2502562 0.00000157 NR A A NR NA COL19A1 SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr6 71429869 rs1727638 0.000000971 NR A A NR NA OGFRL1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr6 71647057 rs9446432 0.0000028 NR NR NR 1.28 1.28 RIMS1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intergenic_region chr6 80806319 rs13213247 0.000024 NR NR NR NR NA BCKDHB SNP-based Disease risk 19118814 Caucasian "CAP, Reiman et al.(2007)" NR All LOAD AD intergenic_region chr6 80806319 rs13213247 0.0000473 NR NR NR NR NA BCKDHB SNP-based Disease risk 19118814 Caucasian CAP 458 All LOAD AD intergenic_region chr6 80806319 rs13213247 0.0159 NR NR NR NR NA BCKDHB SNP-based Disease risk 19118814 Caucasian Reiman et al.(2007) NR All LOAD AD intergenic_region chr6 95766423 rs4642480 0.00000365 NR G G 0.14 1.15027 MANEA SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intergenic_region chr6 104845257 rs79147057 0.0207 HACE1 NR NR NR NA HACE1 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr6 104845257 rs79147057 0.77323 NA NR NR NR NA HACE1 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr6 105037928 rs10457125 0.0128 LIN28B NR NR NR NA LIN28B SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr6 105037928 rs10457125 0.37962 NA NR NR NR NA LIN28B Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr6 106125497 rs4946727 0.0000221 NR NR NR 0.27 0.27 ATG5 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intergenic_region chr6 106129111 rs7761791 0.0000209 NR NR NR 2.38 2.38 ATG5 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intergenic_region chr6 106129632 rs6903903 0.0000276 NR NR NR 0.41 0.41 ATG5 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intergenic_region chr6 108624167 rs2022464 0.0047 NR A A -0.09 0.913931 FOXO3 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 2363 European Intracranial Volume Imaging intron_variant chr6 108624167 rs2022464 0.013 NR A A -0.09 0.913931 FOXO3 SNP-based Endophenotype 27694991 Hispanic "CHARGE, ENIGMA" 1605 Hispanic Intracranial Volume Imaging intron_variant chr6 108624167 rs2022464 0.035 NR A A -0.11 0.895834 FOXO3 SNP-based Endophenotype 27694991 Asian "CHARGE, ENIGMA" 955 Asian Intracranial Volume Imaging intron_variant chr6 108624167 rs2022464 0.233 NR A A -0.06 0.941765 FOXO3 SNP-based Endophenotype 27694991 African American "CHARGE, ENIGMA" 938 African Intracranial Volume Imaging intron_variant chr6 108624167 rs2022464 3.70E-11 NR A A -0.06 0.941765 FOXO3 SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 26577 European Intracranial Volume Imaging intron_variant chr6 109706740 rs2025148 0.0000382 FIG4 NR NR 2.47 2.47 FIG4 SNP-based Disease risk 21098978 Arab Cohort from Israeli 266 All AD AD intron_variant chr6 113138211 rs2502399 0.00000535 LOC102724704 NR NR NR NA MARCKS SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr6 126470949 rs11759026 0.123 NR A A -0.07 0.932394 CENPW SNP-based Endophenotype 27694991 Asian "CHARGE, ENIGMA" 955 Asian Intracranial Volume Imaging intergenic_region chr6 126470949 rs11759026 0.194 NR A A -0.13 0.878095 CENPW SNP-based Endophenotype 27694991 African American "CHARGE, ENIGMA" 938 African Intracranial Volume Imaging intergenic_region chr6 126470949 rs11759026 0.209 NR A A -0.05 0.951229 CENPW SNP-based Endophenotype 27694991 Hispanic "CHARGE, ENIGMA" 1605 Hispanic Intracranial Volume Imaging intergenic_region chr6 126470949 rs11759026 0.528 NR A A -0.02 0.980199 CENPW SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 2363 European Intracranial Volume Imaging intergenic_region chr6 126470949 rs11759026 2.20E-20 NR A A -0.1 0.904837 CENPW SNP-based Endophenotype 27694991 Caucasian "CHARGE, ENIGMA" 26577 European Intracranial Volume Imaging intergenic_region chr6 130961070 rs6941712 0.000000683 EPB41L2 C C -235.78 3.99988e-103 EPB41L2 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr6 130961070 rs6941712 0.00000461 EPB41L2 NR NR -149.67 9.98033e-66 EPB41L2 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr6 130961070 rs6941712 0.11 EPB41L2 C C -72.28 4.06626e-32 EPB41L2 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr6 130961070 rs6941712 0.17 EPB41L2 C C NR NA EPB41L2 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr6 130977259 rs12530288 0.000000682 EPB41L2 T T -235.8 3.92068e-103 EPB41L2 SNP-based Endophenotype 22903471 Caucasian Cohort from Australia 639 All Lentiform nucleus volume Imaging intron_variant chr6 130977259 rs12530288 0.00000976 EPB41L2 NR NR -144.17 2.44211e-63 EPB41L2 SNP-based Endophenotype 22903471 Caucasian "ADNI, Cohort from Australia" 1345 All Lentiform nucleus volume Imaging intron_variant chr6 130977259 rs12530288 0.16 EPB41L2 T T -62.45 7.55631e-28 EPB41L2 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr6 130977259 rs12530288 0.23 EPB41L2 T T NR NA EPB41L2 SNP-based Endophenotype 22903471 Caucasian ADNI 706 All Lentiform nucleus volume Imaging intron_variant chr6 135756791 rs79846291 1.76E-08 "LINC00271, PDE7B" T T 1.85 6.35982 PDE7B SNP-based Endophenotype 29274321 Caucasian ADNI 141 AD Hippocampal volume (HPV) Imaging intergenic_region chr6 137816414 rs679670 0.00000983 NR G G 0.74 0.74 TNFAIP3 SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD intergenic_region chr6 137816414 rs679670 0.016 NR G G 0.87 0.87 TNFAIP3 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD intergenic_region chr6 137816414 rs679670 0.25 NR G G 1.11 1.11 TNFAIP3 SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD intergenic_region chr6 138486144 rs4896367 0.0000014 NR C C 0.49 1.63232 NHSL1 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 138486144 rs4896367 0.011 NR C C 0.16 1.17351 NHSL1 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 138486144 rs4896367 0.62 NR C C -0.04 0.960789 NHSL1 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 142062945 rs6907175 0.00047 LOC651924 NR NR 1.16 1.16 NMBR SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD intron_variant chr6 142062945 rs6907175 0.017 LOC651924 NR NR NR NA NMBR SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD intron_variant chr6 142062945 rs6907175 0.027 LOC651924 A A 1.18 1.18 NMBR SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr6 142062945 rs6907175 0.042 LOC651924 NR NR NR NA NMBR SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD intron_variant chr6 142062945 rs6907175 0.304 LOC651924 NR NR NR NA NMBR SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD intron_variant chr6 142062945 rs6907175 0.957 LOC651924 NR NR NR NA NMBR SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD intron_variant chr6 148102235 rs9390537 0.00000817 SASH1 NR NR NR NA SASH1 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intergenic_region chr6 150713594 rs9371194 0.0000019 PLEKHG1 T T 1.19 1.19 PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 17544 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 150713594 rs9371194 0.0000363 PLEKHG1 T T NR NA PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 17544 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 150713594 rs9371194 0.0000594 PLEKHG1 T T 1.12 1.12 PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 20949 All Brain infarcts (BI) Imaging intron_variant chr6 150713594 rs9371194 0.000428 PLEKHG1 T T NR NA PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 20949 All Brain infarcts (BI) Imaging intron_variant chr6 150713594 rs9371194 0.02 PLEKHG1 NR NR 0.93 0.93 PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 150713594 rs9371194 0.03 PLEKHG1 NR NR 0.94 0.94 PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Brain infarcts (BI) Imaging intron_variant chr6 150713594 rs9371194 0.08 PLEKHG1 NR NR 1.02 1.02 PLEKHG1 SNP-based Endophenotype 30651383 Caucasian "CHARGE, METASTROKE, SiGN" 137560 All Ischemic stroke (IS) Imaging intron_variant chr6 150713594 rs9371194 0.17 PLEKHG1 NR NR 1.03 1.03 PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 24406 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 150713594 rs9371194 0.2 PLEKHG1 NR NR 1.03 1.03 PLEKHG1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 27811 All Brain infarcts (BI) Imaging intron_variant chr6 150713594 rs9371194 0.72 PLEKHG1 NR NR 0.98 0.98 PLEKHG1 SNP-based Endophenotype 30651383 Caucasian ADGC 2940 All Pathologically defined infarcts Imaging intron_variant chr6 150713594 rs9371194 0.75 PLEKHG1 NR NR 1.01 1.01 PLEKHG1 SNP-based Endophenotype 30651383 Caucasian "METASTROKE, SiGN, YLSDR" 41039 All Ischemic stroke due to small vessel disease (IS-SVD) Imaging intron_variant chr6 150885942 rs11754661 0.000000047 MTHFD1L A A 2.03 2.03 MTHFD1L SNP-based Disease risk 20885792 Caucasian "CAP, MSBB, NCRAD" 2035 All LOAD AD intron_variant chr6 150885942 rs11754661 0.0000201 MTHFD1L NR NR NR NA MTHFD1L SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intron_variant chr6 150885942 rs11754661 0.00187 MTHFD1L A A 2.34 2.34 MTHFD1L SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 2979 All LOAD AD intron_variant chr6 150885942 rs11754661 1.90E-10 MTHFD1L A A 2.1 2.1 MTHFD1L SNP-based Disease risk 20885792 Caucasian "ADGC, CAP, CHARGE" 4355 All LOAD AD intron_variant chr6 151818907 rs3844508 0.04 DAPK1 C C 0.81 0.81 ESR1 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1321 All Age of AD onset Other intron_variant chr6 151818907 rs3844508 0.04 ESR1 C C 0.72 0.72 ESR1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1321 All AD AD intron_variant chr6 154432335 rs9397718 0.0000034 NR C C 0.4 1.49182 AL357075.4 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 154432335 rs9397718 0.0014 NR C C 0.18 1.19722 AL357075.4 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 154440150 rs6911312 0.9 NR C C -0.01 0.99005 AL357075.4 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 155254808 rs9397794 0.0000026 NR A A 0.45 1.56831 TIAM2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 363 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 155254808 rs9397794 0.003 NR A A 0.18 1.19722 TIAM2 SNP-based Endophenotype 25027320 Caucasian "ADNI, Cohorts from Europe" 878 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 155254808 rs9397794 0.88 NR A A -0.01 0.99005 TIAM2 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker intron_variant chr6 156178397 rs9384428 0.0000085 NR NR NR 1.14 1.14 ARID1B SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intergenic_region chr6 160295034 rs3103351 0.00000404 SLC22A2 G G NR NA SLC22A2 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intergenic_region chr6 160295034 rs3103351 0.00178 SLC22A2 G G NR NA SLC22A2 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr6 160295034 rs3103351 0.0452 SLC22A2 G G 1 1 SLC22A2 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr6 160608696 rs13202636 0.000000227 LPA NR NR -0.22 0.802519 LPA SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma Lpa Fluid biomarker intron_variant chr6 164151004 rs4145454 0.00000103 NR G G 1.53 NA QKI SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4e3 LOAD AD intergenic_region chr6 168076176 rs75889566 0.00000182 FRMD1 T T 0.65 0.65 FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 10122 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 168076176 rs75889566 0.000044 FRMD1 T T NR NA FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 10122 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 168076176 rs75889566 0.000771 FRMD1 T T 0.82 0.82 FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 15912 All Brain infarcts (BI) Imaging intron_variant chr6 168076176 rs75889566 0.00203 FRMD1 T T NR NA FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 15912 All Brain infarcts (BI) Imaging intron_variant chr6 168076176 rs75889566 0.03 FRMD1 NR NR 0.9 0.9 FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 16984 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 168076176 rs75889566 0.19 FRMD1 NR NR 0.95 0.95 FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 22774 All Brain infarcts (BI) Imaging intron_variant chr6 168076176 rs75889566 0.23 FRMD1 NR NR 1.06 1.06 FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Brain infarcts (BI) Imaging intron_variant chr6 168076176 rs75889566 0.52 FRMD1 NR NR 0.97 0.97 FRMD1 SNP-based Endophenotype 30651383 Caucasian "METASTROKE, SiGN, YLSDR" 41039 All Ischemic stroke due to small vessel disease (IS-SVD) Imaging intron_variant chr6 168076176 rs75889566 0.61 FRMD1 NR NR 1.03 1.03 FRMD1 SNP-based Endophenotype 30651383 Multi-ethnic CHARGE 6862 All Small sub-cortical brain infarcts (SSBI) Imaging intron_variant chr6 168076176 rs75889566 0.67 FRMD1 NR NR 0.99 0.99 FRMD1 SNP-based Endophenotype 30651383 Caucasian "CHARGE, METASTROKE, SiGN" 137560 All Ischemic stroke (IS) Imaging intron_variant chr6 168076176 rs75889566 0.77 FRMD1 NR NR 1.04 1.04 FRMD1 SNP-based Endophenotype 30651383 Caucasian ADGC 2940 All Pathologically defined infarcts Imaging intron_variant chr6 168182326 rs9455973 0.0000447 NR NR NR NR NA FRMD1 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intergenic_region chr7 1512784 rs6942930 0.0000161 NR NR NR NR NA INTS1 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD upstream_gene_variant chr7 5852503 rs117856560 0.015 ZNF815 C C NR NA OCM SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr7 5852503 rs117856560 8.23E-49 NR C C NR NA OCM SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) ZNF815 (ILMN_1700307) expression in peripheral blood Expression intron_variant chr7 6387310 rs702483 0.000311 RAC1 T T NR NA RAC1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All High-density lipoprotein (HDL) Non-ADRD intron_variant chr7 6387310 rs702483 0.000618 RAC1 T T NR NA RAC1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr7 6387310 rs702483 0.0175 RAC1 T T 0.97 0.97 RAC1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr7 6387310 rs702483 0.0317 RAC1 T T 0.97 0.97 RAC1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr7 6387310 rs702483 0.105 RAC1 T T 1 1 RAC1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr7 6387310 rs702483 0.56 RAC1 T T 1.03 1.03 RAC1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr7 10277135 rs10271466 0.00000598 NR NR NR NR NA NDUFA4 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr7 10277135 rs10271466 0.000105 NR NR NR NR NA NDUFA4 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr7 10277135 rs10271466 0.000129 NR NR NR 1.82 1.82 NDUFA4 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr7 10277135 rs10271466 0.00232 NR NR NR 1.52 1.52 NDUFA4 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr7 10277135 rs10271466 0.926 NR NR NR NR NA NDUFA4 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr7 10277135 rs10271466 1 NR NR NR 1.02 1.02 NDUFA4 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr7 10277135 rs10271466 NA NR NR NR NR NA NDUFA4 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr7 10277135 rs10271466 NA NR NR NR NR NA NDUFA4 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr7 12219129 rs3823612 0.00036 TMEM106B NR NR 1.4 1.4 TMEM106B SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (ADD Model) Hippocampal sclerosis of aging ADRD intron_variant chr7 12219129 rs3823612 0.0011 TMEM106B G G 1.53 1.53 TMEM106B SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (REC Model) Hippocampal sclerosis of aging ADRD intron_variant chr7 12228211 rs13229988 0.0062 TMEM106B A A 1.67 1.67 TMEM106B SNP-based Disease risk 28131462 Caucasian ADGC 3251 Individual who died at age 60 or older (DOM Model) Hippocampal sclerosis of aging ADRD intron_variant chr7 12244161 rs1990622 0.049 TMEM106B C C 1.22 1.22 TMEM106B SNP-based Disease risk 24770881 Caucasian ADGC 2239 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 0.132 TMEM106B C C 1.19 1.19 TMEM106B SNP-based Disease risk 24770881 Caucasian ADGC 1636 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 0.198 TMEM106B C C 1.43 1.43 TMEM106B SNP-based Disease risk 24770881 Caucasian ADGC 427 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 0.528 TMEM106B C C 1.24 1.24 TMEM106B SNP-based Disease risk 24770881 Caucasian ADGC 176 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 NR ABCC9 A A 1.16 1.16 TMEM106B SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 NR ABCC9 A A 1.18 1.18 TMEM106B SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 NR ABCC9 A A 1.24 1.24 TMEM106B SNP-based Disease risk 25470345 Caucasian ADGC 2343 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 NR ABCC9 A A 1.86 1.86 TMEM106B SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 NR ABCC9 A A 2.14 2.14 TMEM106B SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 12244161 rs1990622 NR ABCC9 A A 2.7 2.7 TMEM106B SNP-based Disease risk 25470345 Caucasian ADGC 612 All Hippocampal sclerosis of aging (HS-Aging) ADRD downstream_gene_variant chr7 14848793 rs1117750 0.00000802 DGKB NR NR NR NA DGKB SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr7 14848793 rs1117750 0.000192 NR NR NR 7.87 7.87 DGKB SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr7 14848793 rs1117750 0.00131 DGKB NR NR NR NA DGKB SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr7 14848793 rs1117750 0.00286 DGKB NR NR NR NA DGKB SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr7 14848793 rs1117750 0.0279 NR NR NR 2.29 2.29 DGKB SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr7 14848793 rs1117750 0.04563 DGKB NR NR NR NA DGKB SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr7 14848793 rs1117750 0.0575 NR NR NR 1.67 1.67 DGKB SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr7 14848793 rs1117750 0.26433 DGKB NR NR NR NA DGKB SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr7 14848793 rs1117750 0.953 DGKB NR NR NR NA DGKB SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr7 16722846 rs34331204 0.001 NR NR NR 0.27 1.30996 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Males Executive function Cognitive upstream_gene_variant chr7 16722846 rs34331204 0.014 NR NR NR 252.17 32812513659558208417555928632904064147678450779683213019144254492454938840143200706111188441476454794743775232 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Males Hippocampal volume Imaging upstream_gene_variant chr7 16722846 rs34331204 0.052 NR NR NR -0.09 0.913931 BZW2 SNP-based Age at onset (AAO) / Survival 31497858 Caucasian ADGC NR Males Age of onset in ADGC Other upstream_gene_variant chr7 16722846 rs34331204 0.14 NR NR NR 0.1 1.10517 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Males Episodic memory Cognitive upstream_gene_variant chr7 16722846 rs34331204 0.27 NR NR NR 0.04 1.04081 BZW2 SNP-based Age at onset (AAO) / Survival 31497858 Caucasian ADGC NR Females Age of onset in ADGC Other upstream_gene_variant chr7 16722846 rs34331204 0.35 NR NR NR 0.08 1.08329 BZW2 SNP-based Age at onset (AAO) / Survival 31497858 Caucasian ADGC NR Females Age of onset in CERAD Other upstream_gene_variant chr7 16722846 rs34331204 0.47 NR NR NR -0.01 0.99005 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Females CSF P-tau181p Fluid biomarker upstream_gene_variant chr7 16722846 rs34331204 0.47 NR NR NR 0.08 1.08329 BZW2 SNP-based Age at onset (AAO) / Survival 31497858 Caucasian ADGC NR Males Age of onset in CERAD Other upstream_gene_variant chr7 16722846 rs34331204 0.58 NR NR NR -0.01 0.99005 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Females CSF T-tau Fluid biomarker upstream_gene_variant chr7 16722846 rs34331204 0.69 NR NR NR 0.01 1.01005 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Males CSF T-tau Fluid biomarker upstream_gene_variant chr7 16722846 rs34331204 0.73 NR NR NR 0.04 1.04081 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Females Episodic memory Cognitive upstream_gene_variant chr7 16722846 rs34331204 0.8 NR NR NR -33.18 3.89143e-15 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Females Hippocampal volume Imaging upstream_gene_variant chr7 16722846 rs34331204 0.88 NR NR NR -0.02 0.980199 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Females Executive function Cognitive upstream_gene_variant chr7 16722846 rs34331204 0.89 NR NR NR 0 1 BZW2 SNP-based Endophenotype 31497858 Caucasian ADGC NR Males CSF P-tau181p Fluid biomarker upstream_gene_variant chr7 18658708 rs79524815 0.000000011 HDAC9 NR NR NR NA HDAC9 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neurofibrillary tangles (NFT)+Cerebral amyloid angiopathy (CAA) Neuropathology intron_variant chr7 18658708 rs79524815 0.0000033 HDAC9 NR NR NR NA HDAC9 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neuritic plaque (NP)+Cerebral amyloid angiopathy (CAA) Neuropathology intron_variant chr7 18658708 rs79524815 0.0000091 HDAC9 NR NR 1.16 3.18993 HDAC9 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Cerebral amyloid angiopathy (CAA) Neuropathology intron_variant chr7 18658708 rs79524815 0.000023 HDAC9 NR NR 0.79 2.2034 HDAC9 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neurofibrillary tangles (NFT) Neuropathology intron_variant chr7 18658708 rs79524815 0.00013 HDAC9 NR NR NR NA HDAC9 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neuritic plaque (NP)+Neurofibrillary tangles (NFT) Neuropathology intron_variant chr7 18658708 rs79524815 0.03 HDAC9 NR NR 0.43 1.53726 HDAC9 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All Neuritic plaque (NP) Neuropathology intron_variant chr7 18658708 rs79524815 0.03 HDAC9 NR NR 0.69 1.99372 HDAC9 SNP-based Pleiotropy 29458411 Caucasian ADGC 3598 All AD AD intron_variant chr7 19161192 rs11766540 0.0000193 NR NR NR 2.27 2.27 FERD3L SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr7 19161192 rs11766540 0.000246 NR NR NR 2.14 2.14 FERD3L SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr7 19161192 rs11766540 0.013 NR NR NR 2.09 2.09 FERD3L SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr7 19161192 rs11766540 0.185 NR NR NR 1.38 1.38 FERD3L SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr7 22665007 rs57375391 0.00000158 LOC401312 NR NR 0.497 1.64378 STEAP1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr7 22665007 rs57375391 0.000129 LOC401312 NR NR 0.514 1.67197 STEAP1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr7 22665007 rs57375391 0.00105 LOC401312 NR NR 0.539 1.71429 STEAP1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr7 22727026 rs1800795 0.000000074 IL6 NR NR 0.38 1.46228 STEAP1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr7 22727026 rs1800795 0.00000994 IL6 NR NR 0.24 1.27125 STEAP1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr7 22727026 rs1800795 0.785 IL6 NR NR 0.02 1.0202 STEAP1B SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr7 23530965 rs1046135 0.00189 TRA2A T T NR NA TRA2A SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr7 23530965 rs1046135 4.32E-115 NR T T NR NA TRA2A SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) TRA2A (ILMN_1731043) expression in peripheral blood Expression intron_variant chr7 25679184 rs1859849 0.00058 NR NR NR 1.15 1.15 NPVF SNP-based Disease risk 17317784 Caucasian Cohorts from UK 3870 All LOAD AD intron_variant chr7 25679184 rs1859849 0.0047 NR NR NR NR NA NPVF SNP-based Disease risk 17317784 Caucasian Cohorts from UK 776 All LOAD AD intron_variant chr7 25679184 rs1859849 0.031 NR NR NR NR NA NPVF SNP-based Disease risk 17317784 Caucasian Cohorts from UK 658 All LOAD AD intron_variant chr7 25679184 rs1859849 0.168 NR NR NR NR NA NPVF SNP-based Disease risk 17317784 Caucasian Cohorts from UK 720 All LOAD AD intron_variant chr7 25679184 rs1859849 0.575 NR NR NR NR NA NPVF SNP-based Disease risk 17317784 Caucasian Cohorts from UK 1146 All LOAD AD intron_variant chr7 25679184 rs1859849 0.776 NR NR NR NR NA NPVF SNP-based Disease risk 17317784 Caucasian Cohorts from UK 570 All LOAD AD intron_variant chr7 28102567 rs10245867 0.00000022 JAZF1 NR NR NR NA JAZF1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr7 28105182 rs1109484 0.000013 JAZF1 NR NR NR NA JAZF1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr7 28156794 rs849135 3.40E-10 JAZF1 NR NR NR NA JAZF1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr7 28184434 rs849336 4.80E-09 LOC100128081 NR NR NR NA JAZF1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr7 28216621 rs498475 8.80E-09 LOC100128081 NR NR NR NA JAZF1 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr7 29030593 rs7313 1.06E-36 CPVL NR NR -0.88 0.414783 CPVL SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD CPVL expression in Cerebellar Expression missense_variant chr7 29030593 rs7313 1.55E-67 CPVL NR NR -1.34 0.261846 CPVL SNP-based eQTL 22685416 Caucasian MAYO 399 All CPVL expression in Temporal cortex Expression missense_variant chr7 29030593 rs7313 2.22E-86 CPVL NR NR -0.96 0.382893 CPVL SNP-based eQTL 22685416 Caucasian MAYO 374 All CPVL expression in Cerebellar Expression missense_variant chr7 29030593 rs7313 9.48E-44 CPVL NR NR -1.01 0.364219 CPVL SNP-based eQTL 22685416 Caucasian MAYO 197 AD CPVL expression in Cerebellar Expression missense_variant chr7 29201829 rs121724 0.000000145 CHN2 G G NR NA AC004593.2 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF P-tau181p Fluid biomarker intron_variant chr7 31952112 rs73310519 0.00000886 PDE1C NR NR NR NA PDE1C SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intron_variant chr7 37580319 rs17265593 0.00025 BC043356 NR NR -0.23 NA GPR141 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intergenic_region chr7 37650904 rs2597283 0.000000167 BC043356 C C 0.93 0.93 GPR141 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intergenic_region chr7 37650904 rs2597283 0.00000165 BC043356 C C 0.94 0.94 GPR141 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intergenic_region chr7 37650904 rs2597283 0.00002 BC043356 NR NR 0.28 NA GPR141 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intergenic_region chr7 37650904 rs2597283 0.000042 BC043356 C C NR NA GPR141 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr7 37650904 rs2597283 0.000346 BC043356 C C NR NA GPR141 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intergenic_region chr7 37650904 rs2597283 0.0648 BC043356 C C 1 1 GPR141 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr7 37650904 rs2597283 0.353 BC043356 C C 1.05 1.05 GPR141 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intergenic_region chr7 37801932 rs2718058 0.000013 NME8 G G 0.93 0.93 GPR141 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr7 37801932 rs2718058 0.000063 NME8 G G 0.91 0.91 GPR141 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr7 37801932 rs2718058 0.0023 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in substantia nigra (SNIG) Expression intron_variant chr7 37801932 rs2718058 0.0075 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 37801932 rs2718058 0.0085 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in putamen (PUTM) Expression intron_variant chr7 37801932 rs2718058 0.02 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in frontal cortex (FCTX) Expression intron_variant chr7 37801932 rs2718058 0.05 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in hippocampus (HIPP) Expression intron_variant chr7 37801932 rs2718058 0.11 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in temporal cortex (TCTX) Expression intron_variant chr7 37801932 rs2718058 0.12 NME8 G G 1.081 1.081 GPR141 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr7 37801932 rs2718058 0.17 NME8 NR NR 1.12 1.12 GPR141 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr7 37801932 rs2718058 0.23 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in substantia nigra (SNIG) Expression intron_variant chr7 37801932 rs2718058 0.29 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in putamen (PUTM) Expression intron_variant chr7 37801932 rs2718058 0.3 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in thalamus (THAL) Expression intron_variant chr7 37801932 rs2718058 0.33 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in medulla (MEDU) Expression intron_variant chr7 37801932 rs2718058 0.35 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in hippocampus (HIPP) Expression intron_variant chr7 37801932 rs2718058 0.39 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in occipital cortex (OCTX) Expression intron_variant chr7 37801932 rs2718058 0.43 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 37801932 rs2718058 0.47 NME8 G G 0.95 0.95 GPR141 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr7 37801932 rs2718058 0.51 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in temporal cortex (TCTX) Expression intron_variant chr7 37801932 rs2718058 0.55 NME8 G G 0.96 0.96 GPR141 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr7 37801932 rs2718058 0.64 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 37801932 rs2718058 0.65 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in occipital cortex (OCTX) Expression intron_variant chr7 37801932 rs2718058 0.67 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 37801932 rs2718058 0.8 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in frontal cortex (FCTX) Expression intron_variant chr7 37801932 rs2718058 0.95 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997791) expression in thalamus (THAL) Expression intron_variant chr7 37801932 rs2718058 0.98 GPR141 NR NR NR NA GPR141 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GPR141 (2997812) expression in medulla (MEDU) Expression intron_variant chr7 37801932 rs2718058 4.80E-09 NME8 G G 0.93 0.93 GPR141 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr7 37801932 rs2718058 NR NME8 A A 0.77 0.77 GPR141 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 37801932 rs2718058 NR ZCWPW1 A A 0.743 0.743 GPR141 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 37801932 rs2718058 NR ZCWPW1 A A 0.89 0.89 GPR141 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 37804661 rs4723711 0.00000028 NME8 T T 0.94 0.94 GPR141 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr7 37804661 rs4723711 0.0001 NME8 T T 0.91 0.91 GPR141 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr7 37804661 rs4723711 0.00027 NME8 T T 0.95 0.95 GPR141 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr7 37861400 rs17171184 0.0257 NME8 G G 0.84 NA EPDR1 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr7 48193794 rs144495862 0.00000922 ABCA13 NR NR 0.422 1.52501 ABCA13 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr7 48193794 rs144495862 0.00117 ABCA13 NR NR 0.545 1.72461 ABCA13 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr7 48193794 rs144495862 0.0028 ABCA13 NR NR 0.363 1.43764 ABCA13 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr7 51075908 rs1437490 0.0043 COBL NR NR NR NA COBL SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr7 51510325 rs112404845 0.000000128 COBL T T 0.46 1.58407 COBL SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD liability score AD intergenic_region chr7 51510325 rs112404845 0.00000087 COBL T T 3.59 3.59 COBL SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD AD intergenic_region chr7 51510325 rs112404845 0.00000122 COBL T T 3.28 3.28 COBL SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD AD intergenic_region chr7 51510325 rs112404845 3.82E-08 COBL T T 0.47 1.59999 COBL SNP-based Disease risk 27770636 African American ADGC 5609 All LOAD liability score AD intergenic_region chr7 55124563 rs13244925 0.000000912 EGFR NR NR 0.25 1.28403 EGFR SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma EGFR Fluid biomarker intron_variant chr7 71417177 rs7798395 0.0000022 WBSCR17 C C NR NA GALNT17 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr7 71417177 rs7798395 0.0009 WBSCR17 C C NR NA GALNT17 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr7 71417177 rs7798395 0.0011 WBSCR17 C C NR NA GALNT17 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr7 88777238 rs73705514 2.86E-09 ZNF804B C C -0.84 0.431711 ZNF804B SNP-based Endophenotype 29274321 Caucasian ADNI 581 MCI Logic memory delayed (LMdT) recall test Cognitive intron_variant chr7 90631335 rs17867001 0.0101 CDK14 G G NR NA CDK14 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr7 90631335 rs17867001 4.63E-17 NR G G NR NA CDK14 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group CDK14 (ENSG00000223969) expression Expression intron_variant chr7 91274325 rs9942607 0.00000939 FZD1 NR NR NR NA FZD1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr7 91274344 rs9942608 0.00000939 FZD1 NR NR NR NA FZD1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr7 91275623 rs10252817 0.00000939 FZD1 NR NR NR NA FZD1 SNP-based Endophenotype 22821396 Caucasian "ADNI, Knight-ADRC" 570 All CSF APOE Fluid biomarker intergenic_region chr7 91957075 rs756647 0.0248 AKAP9 NR NR NR NA AKAP9 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr7 92079771 rs144662445 0.0022 AKAP9 NR NR 2.75 2.75 AKAP9 SNP-based Disease risk 25172201 African American ADGC 2906 All AD AD missense_variant chr7 92079771 rs144662445 0.014 AKAP9 NR NR NR NA AKAP9 SNP-based Disease risk 25172201 African American ADGC 816 All AD AD missense_variant chr7 92102796 rs149979685 0.0022 AKAP9 NR NR 3.61 3.61 AKAP9 SNP-based Disease risk 25172201 African American ADGC 2906 All AD AD missense_variant chr7 92102796 rs149979685 0.037 AKAP9 NR NR NR NA AKAP9 SNP-based Disease risk 25172201 African American ADGC 816 All AD AD missense_variant chr7 92117413 rs2301559 0.0419 CYP51A1 NR NR NR NA CYP51A1 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chr7 95320351 rs2299261 0.03 PON1 G G 1.33 1.33 PON1 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1388 All Age of AD onset Other intron_variant chr7 95320351 rs2299261 0.36 PON1 G G 1.33 1.33 PON1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1388 All AD AD intron_variant chr7 99875063 rs35649099 0.203 OR2AE1 NR NR 0.01422 1.01432 OR2AE1 SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker downstream_gene_variant chr7 100131167 rs35991721 0.000000262 MBLAC1 T T 0.93 0.93 MBLAC1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr7 100131167 rs35991721 0.00000322 MBLAC1 T T NR NA MBLAC1 SNP-based Cross phenotype 30413934 Caucasian CARDIoGRAMplusC4D 155197 All Coronary artery disease (CAD) Non-ADRD intron_variant chr7 100131167 rs35991721 0.0000577 MBLAC1 T T NR NA MBLAC1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr7 100131167 rs35991721 0.000234 MBLAC1 T T 0.99 0.99 MBLAC1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr7 100131167 rs35991721 0.000717 MBLAC1 T T 0.83 0.83 MBLAC1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr7 100131167 rs35991721 5.32E-09 MBLAC1 T T 0.92 0.92 MBLAC1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr7 100176704 rs12705074 0.0384 GPC2 NR NR 0.01702 1.01717 GPC2 SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr7 100223178 rs150436753 0.122 MGC2463 NR NR 0.02 1.0202 CASTOR3 SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr7 100334426 rs7384878 2.38E-10 ZCWPW1 A A NR NA SPDYE3 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr7 100363571 rs6955367 2.13E-91 PILRB NR NR 1.08 2.94468 PILRB SNP-based eQTL 22685416 Caucasian MAYO 374 All PILRB expression in Cerebellar Expression intron_variant chr7 100363571 rs6955367 3.89E-43 PILRB NR NR 0.99 2.69123 PILRB SNP-based eQTL 22685416 Caucasian MAYO 197 AD PILRB expression in Cerebellar Expression intron_variant chr7 100363571 rs6955367 4.56E-138 PILRB NR NR 1.56 4.75882 PILRB SNP-based eQTL 22685416 Caucasian MAYO 399 All PILRB expression in Temporal cortex Expression intron_variant chr7 100363571 rs6955367 6.99E-47 PILRB NR NR 1.21 3.35348 PILRB SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD PILRB expression in Cerebellar Expression intron_variant chr7 100373690 rs2405442 0.00212 ZCWPW1 NR NR 0.92 0.92 PILRA SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD synonymous_variant chr7 100374211 rs1859788 0.00562 ZCWPW1 NR NR 0.93 0.93 PILRA SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD missense_variant chr7 100374211 rs1859788 2.22E-15 ZCWPW1 A A -7.93 NA PILRA SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD missense_variant chr7 100374211 rs1859788 6.05E-09 ZCWPW1 A A NR NA PILRA SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD missense_variant chr7 100380783 rs28714213 0.0171 PILRA NR NR 0.017 1.01715 PILRA SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr7 100406823 rs1476679 0.00000023 ZCWPW1 NR NR 0.15 1.16183 ZCWPW1 SNP-based eQTL 30448613 Caucasian ADNI 763 All ZKSCAN1 (11760665_at) expression in blood Expression intron_variant chr7 100406823 rs1476679 0.0000074 ZCWPW1 C C 0.92 0.92 ZCWPW1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr7 100406823 rs1476679 0.0000097 ZCWPW1 C C 0.89 0.89 ZCWPW1 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr7 100406823 rs1476679 0.0000126 ZCWPW1 NR NR 0.11 NA ZCWPW1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr7 100406823 rs1476679 0.0000607 ZCWPW1 NR NR 0.09 1.09417 ZCWPW1 SNP-based eQTL 30448613 Caucasian ADNI 763 All PVRIG (11730247_a_at) expression in blood Expression intron_variant chr7 100406823 rs1476679 0.00035 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.00042 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.00058 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.00059 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.00064 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.000655 ZCWPW1 C C 0.846 0.846 ZCWPW1 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr7 100406823 rs1476679 0.00083 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.00095 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.0011 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.0011 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.0012 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.0013 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.00141 ZCWPW1 NR NR 0.92 0.92 ZCWPW1 SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD intron_variant chr7 100406823 rs1476679 0.0016 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.0022 ZCWPW1 NR NR 0.109 1.11516 ZCWPW1 SNP-based eQTL 26919393 Caucasian "UM, NACC" 364 All PILRB expression in Brain Expression intron_variant chr7 100406823 rs1476679 0.0023 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.0031 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.0031 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.0056 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.0099 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.0099 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.01 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.01 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.018 ZCWPW1 C C 0.86 0.86 ZCWPW1 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr7 100406823 rs1476679 0.02 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.02 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.02 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.023 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.03 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.03 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.04 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.04 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.04 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.04 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.043 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.045 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.05 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.06 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.06 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.06 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.06 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.061 ZCWPW1 C C 0.86 0.86 ZCWPW1 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr7 100406823 rs1476679 0.07 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.07 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.09 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.094 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.1 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.1 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.12 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015527) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.12 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.13 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.14 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.16 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.16 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.16 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.2 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.2 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.23 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.23 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.24 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.24 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.24 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.28 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.28 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.29 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.29 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.3 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015452) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.3 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.32 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.33 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.33 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.34 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.34 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.36 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015442) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.36 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.39 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.43 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.5 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.5 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.52 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.55 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.56 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.58 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.59 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.59 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.65 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.66 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in temporal cortex (TCTX) Expression intron_variant chr7 100406823 rs1476679 0.67 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.68 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.68 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.7 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in occipital cortex (OCTX) Expression intron_variant chr7 100406823 rs1476679 0.7 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.72 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.72 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.73 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063856) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.73 ZCWPW1 NR NR 1.05 1.05 ZCWPW1 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr7 100406823 rs1476679 0.74 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.74 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in intra-locular white matter (WHMT) Expression intron_variant chr7 100406823 rs1476679 0.76 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.77 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.78 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.78 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.78 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.78 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in substantia nigra (SNIG) Expression intron_variant chr7 100406823 rs1476679 0.82 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in medulla (MEDU) Expression intron_variant chr7 100406823 rs1476679 0.83 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.84 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (3063971) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.9 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.9 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 0.9 ZCWPW1 NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects ZCWPW1 (t3063968) expression in hippocampus (HIPP) Expression intron_variant chr7 100406823 rs1476679 0.91 "PILRA, PILRB" NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB/PILRA (3015536) expression in cerebellar cortex (CRBL) Expression intron_variant chr7 100406823 rs1476679 0.91 GATS NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects GATS (3063857) expression in thalamus (THAL) Expression intron_variant chr7 100406823 rs1476679 0.93 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.94 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015543) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.94 PILRA NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRA (3015544) expression in putamen (PUTM) Expression intron_variant chr7 100406823 rs1476679 0.94 PILRB NR NR NR NA ZCWPW1 SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects PILRB (3015476) expression in frontal cortex (FCTX) Expression intron_variant chr7 100406823 rs1476679 1.53E-17 ZCWPW1 NR NR 0.18 1.19722 ZCWPW1 SNP-based eQTL 30448613 Caucasian ADNI 763 All GATS (11722909_a_at) expression in blood Expression intron_variant chr7 100406823 rs1476679 1.58E-08 ZCWPW1 NR NR 0.107 1.11293 ZCWPW1 SNP-based eQTL 30448613 Caucasian ADNI 763 All PILRB (11730023 s at) expression in blood Expression intron_variant chr7 100406823 rs1476679 3.53E-09 ZCWPW1 NR NR 0.129 1.13769 ZCWPW1 SNP-based eQTL 30448613 Caucasian ADNI 763 All TRIM4 (11736388_a_at) expression in blood Expression intron_variant chr7 100406823 rs1476679 3.77E-08 ZCWPW1 NR NR 0.128 1.13655 ZCWPW1 SNP-based eQTL 30448613 Caucasian ADNI 763 All PILRB (11730022_a_at) expression in blood Expression intron_variant chr7 100406823 rs1476679 4.15E-09 ZCWPW1 NR NR 0.115 1.12187 ZCWPW1 SNP-based eQTL 30448613 Caucasian ADNI 763 All PILRB (11743311_a_at) expression in blood Expression intron_variant chr7 100406823 rs1476679 5.60E-10 ZCWPW1 C C 0.91 0.91 ZCWPW1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr7 100406823 rs1476679 NR ZCWPW1 T T 1.04 1.04 ZCWPW1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 100406823 rs1476679 NR ZCWPW1 T T 1.31 1.31 ZCWPW1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 100406823 rs1476679 NR ZCWPW1 T T 2.98 2.98 ZCWPW1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 100415834 rs5015756 0.0000326 PILRB NR NR 0.081 1.08437 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1723984) expression in Frontal Cortex Expression intron_variant chr7 100415834 rs5015756 0.0000412 PILRB NR NR 0.058 1.05971 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1723984) expression in Temporal cortex Expression intron_variant chr7 100415834 rs5015756 0.0000565 PILRB NR NR 0.068 1.07037 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1685534) expression in Frontal Cortex Expression intron_variant chr7 100415834 rs5015756 0.0182 PILRB NR NR 0.104 1.1096 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1768754) expression in Temporal cortex Expression intron_variant chr7 100415834 rs5015756 0.0257 PILRB NR NR 0.031 1.03149 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1663753) expression in Temporal cortex Expression intron_variant chr7 100415834 rs5015756 0.0384 PILRB NR NR 0.046 1.04707 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1760345) expression in Frontal Cortex Expression intron_variant chr7 100415834 rs5015756 0.0572 PILRB NR NR 0.027 1.02737 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1685534) expression in Temporal cortex Expression intron_variant chr7 100415834 rs5015756 0.0732 PILRB NR NR 0.021 1.02122 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1663753) expression in Frontal Cortex Expression intron_variant chr7 100415834 rs5015756 0.29 PILRB NR NR 0.038 1.03873 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1768754) expression in Frontal Cortex Expression intron_variant chr7 100415834 rs5015756 0.338 ZCWPW1 A A 1.06 NA ZCWPW1 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr7 100415834 rs5015756 0.436 PILRB NR NR 0.01 1.01005 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1760345) expression in Temporal cortex Expression intron_variant chr7 100415834 rs5015756 0.524 PILRB NR NR 0.008 1.00803 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1729915) expression in Temporal cortex Expression intron_variant chr7 100415834 rs5015756 0.71 PILRB NR NR -0.005 0.995012 ZCWPW1 SNP-based eQTL 26919393 Caucasian "JHU, UM" 150 Healthy subjects PILRB (ILMN_1729915) expression in Frontal Cortex Expression intron_variant chr7 100494172 rs12539172 0.0000021 NYAP1 T T 0.89 0.89 NYAP1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD 3_prime_UTR_variant chr7 100494172 rs12539172 0.000021 NYAP1 T T 0.93 0.93 NYAP1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD 3_prime_UTR_variant chr7 100494172 rs12539172 9.30E-10 NYAP1 T T 0.92 0.92 NYAP1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD 3_prime_UTR_variant chr7 100565492 rs78951820 0.0247 AGFG2 NR NR 0.03433 1.03493 AGFG2 SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker 3_prime_UTR_variant chr7 101103377 rs10953322 0.00000465 TRIM56 G G 0.76 0.76 TRIM56 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intergenic_region chr7 101161149 rs1048365 0.0000784 AP1S1 T T NR NA AP1S1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD 3_prime_UTR_variant chr7 101161149 rs1048365 0.000222 AP1S1 T T NR NA AP1S1 SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD 3_prime_UTR_variant chr7 101161149 rs1048365 0.945 AP1S1 T T 1 1 AP1S1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD 3_prime_UTR_variant chr7 103958224 rs6943822 0.0783 RELN NR NR NR NA RELN SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr7 103958224 rs6943822 0.446 RELN NR NR NR NA RELN SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr7 103985430 rs4298437 0.0162 RELN NR NR NR NA RELN SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr7 103985430 rs4298437 0.0341 RELN NR NR NR NA RELN SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr7 108346641 rs10487849 1.36E-08 NRCAM NR NR 0.06 1.06184 NRCAM SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma Nr-CAM Fluid biomarker intron_variant chr7 122377758 rs1859351 0.00016 CADPS2 NR NR NR NA CADPS2 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr7 129028456 rs10239340 1.01E-86 IRF5 NR NR 0.92 2.50929 TNPO3 SNP-based eQTL 22685416 Caucasian MAYO 399 All IRF5 expression in Temporal cortex Expression intron_variant chr7 129028456 rs10239340 2.59E-27 IRF5 NR NR 0.81 2.24791 TNPO3 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD IRF5 expression in Cerebellar Expression intron_variant chr7 129028456 rs10239340 3.32E-38 IRF5 NR NR 0.82 2.2705 TNPO3 SNP-based eQTL 22685416 Caucasian MAYO 197 AD IRF5 expression in Cerebellar Expression intron_variant chr7 129028456 rs10239340 6.73E-71 IRF5 NR NR 0.81 2.24791 TNPO3 SNP-based eQTL 22685416 Caucasian MAYO 374 All IRF5 expression in Cerebellar Expression intron_variant chr7 130748625 rs4731702 0.0000002 KLF14 NR NR NR NA KLF14 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr7 130753455 rs13234407 0.00000029 KLF14 NR NR NR NA KLF14 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr7 131603231 rs12534221 0.000000904 NR A A NR NA PODXL SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF Ab1-42 Fluid biomarker intergenic_region chr7 132352924 rs12539196 0.000028 PLXNA4 A A NR NA PLXNA4 SNP-based Disease risk 25043464 Caucasian "ADGC, CHARGE" 6704 All AD AD intron_variant chr7 132426164 rs277470 0.000000041 PLXNA4 C C NR NA PLXNA4 SNP-based Disease risk 25043464 Caucasian "ADGC, CHARGE" 6704 All AD AD intron_variant chr7 143402040 rs10808026 0.000000031 EPHA1 A A 0.9 0.9 EPHA1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr7 143402040 rs10808026 0.0011 EPHA1 A A 0.91 0.91 EPHA1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr7 143402040 rs10808026 1.30E-10 EPHA1 A A 0.9 0.9 EPHA1 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr7 143410495 rs12703526 6.91E-08 "EPHA1, TAS2R62P" NR NR NR NA EPHA1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr7 143410783 rs11762262 0.034 EPHA1 T T 1.27 1.27 EPHA1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr7 143411065 rs7810606 0.00000101 EPHA1 T T NR NA EPHA1 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr7 143411065 rs7810606 3.59E-11 EPHA1 T T -6.62 NA EPHA1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr7 143411748 rs11763230 2.58E-11 EPHA1 T T NR NA EPHA1 SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr7 143412046 rs11767557 0.000000049 EPHA1 C C 0.87 0.87 EPHA1 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr7 143412046 rs11767557 0.000000243 EPHA1 C C 0.87 0.87 EPHA1 SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr7 143412046 rs11767557 0.00029 EPHA1 NR NR 0.91 0.91 EPHA1 SNP-based Disease risk 21460841 Caucasian "CHARGE, EADI, GERAD" 25818 All LOAD AD intron_variant chr7 143412046 rs11767557 0.00034 EPHA1 NR NR 0.9 0.9 EPHA1 SNP-based Disease risk 21460840 Caucasian "EADI, GERAD" 19218 All AD AD intron_variant chr7 143412046 rs11767557 0.133 EPHA1 C C 0.93 0.93 EPHA1 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr7 143412046 rs11767557 0.169 EPHA1 C C 0.94 0.94 EPHA1 SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr7 143412046 rs11767557 0.39 EPHA1 NR NR 0.92 0.92 EPHA1 SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr7 143412046 rs11767557 0.555 NR C C 0.02 1.0202 EPHA1 SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology intron_variant chr7 143412046 rs11767557 0.586 EPHA1 C C 1.06 1.06 EPHA1 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr7 143412046 rs11767557 0.647 EPHA1 C C 1.03 1.03 EPHA1 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr7 143412046 rs11767557 0.659 EPHA1 C C 0.07 1.07251 EPHA1 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr7 143412046 rs11767557 0.83 EPHA1 C C 0.03 1.03045 EPHA1 SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr7 143412046 rs11767557 3.06E-08 EPHA1 C C 0.84 0.84 EPHA1 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr7 143412046 rs11767557 6.00E-10 EPHA1 NR NR 0.9 0.9 EPHA1 SNP-based Disease risk 21460840 Caucasian "ADGC, GERAD" NR All AD AD intron_variant chr7 143412046 rs11767557 6.00E-10 EPHA1 NR NR 0.9 0.9 EPHA1 SNP-based Disease risk 21460841 Caucasian "ADGC, CHARGE, EADI, GERAD" 48589 All LOAD AD intron_variant chr7 143412046 rs11767557 7.33E-08 EPHA1 C C 0.85 0.85 EPHA1 SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr7 143413669 rs11771145 0.0000017 EPHA1 A A 0.91 0.91 EPHA1 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intron_variant chr7 143413669 rs11771145 0.00000368 EPHA1 NR NR 0.11 1.11628 EPHA1 SNP-based eQTL 30448613 Caucasian ADNI 763 All LOC154761 (11755327 s at) expression in blood Expression intron_variant chr7 143413669 rs11771145 0.000028 EPHA1 A A 0.9 0.9 EPHA1 SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr7 143413669 rs11771145 0.000214 EPHA1 A A 0.87 0.87 EPHA1 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intron_variant chr7 143413669 rs11771145 0.073 EPHA1 A A 0.89 0.89 EPHA1 SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr7 143413669 rs11771145 0.091 EPHA1 A A 0.88 0.88 EPHA1 SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr7 143413669 rs11771145 1.10E-13 EPHA1 A A 0.9 0.9 EPHA1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr7 143413669 rs11771145 1.32E-08 EPHA1 A A 0.86 0.86 EPHA1 SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intron_variant chr7 143413669 rs11771145 8.80E-10 EPHA1 A A 0.9 0.9 EPHA1 SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr7 143413669 rs11771145 NR EPHA1 G G 0.96 0.96 EPHA1 SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 143413669 rs11771145 NR ZCWPW1 G G 0.88 0.88 EPHA1 SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 143413669 rs11771145 NR ZCWPW1 G G 1.29 1.29 EPHA1 SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr7 143425364 rs10226151 5.91E-09 "EPHA1, TAS2R62P" NR NR NR NA EPHA1 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr7 143425831 rs78571833 0.000158 AL833583 NR NR 0.14 NA EPHA1 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr7 143444382 rs4595035 0.0094 EPHA1 T T 1.25 1.25 TAS2R60 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD synonymous_variant chr7 146252937 rs114360492 2.10E-09 CNTNAP2 T T 5.99 NA CNTNAP2 SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr7 146265094 rs802571 0.00000126 CNTNAP2 C C 0.52 0.52 CNTNAP2 SNP-based Disease risk 26049409 Asian Cohort from Japan 13296 e4 noncarrier LOAD AD intron_variant chr7 146265094 rs802571 0.0000314 CNTNAP2 C C 0.36 0.36 CNTNAP2 SNP-based Disease risk 26049409 Asian Cohort from Japan 6948 e4 noncarrier LOAD AD intron_variant chr7 146265094 rs802571 0.00208 CNTNAP2 C C 0.61 0.61 CNTNAP2 SNP-based Disease risk 26049409 Asian Cohort from Japan 6348 e4 noncarrier LOAD AD intron_variant chr7 147200311 rs10273775 0.00000894 CNTNAP2 G G 1.52 1.52 CNTNAP2 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr7 150521029 rs73726888 4.21E-09 GIMAP7 NR NR NR NA GIMAP7 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker 3_prime_UTR_variant chr7 150521029 rs73726888 6.44E-24 GIMAP7 NR NR NR NA GIMAP7 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker 3_prime_UTR_variant chr8 4005589 rs17068510 0.00000796 CSMD1 NR NR 0.29 1.33643 CSMD1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr8 4005589 rs17068510 0.000341 CSMD1 NR NR 0.33 1.39097 CSMD1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr8 4005589 rs17068510 0.0081 CSMD1 NR NR 0.25 1.28403 CSMD1 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr8 4543602 rs11786902 0.00000867 NR NR NR NR NA CSMD1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr8 4543602 rs11786902 0.000134 NR NR NR NR NA CSMD1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr8 4543602 rs11786902 0.00019 NR NR NR 0.59 0.59 CSMD1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr8 4543602 rs11786902 0.00311 NR NR NR 0.69 0.69 CSMD1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr8 4543602 rs11786902 0.09129 NR NR NR NR NA CSMD1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr8 4543602 rs11786902 0.43359 NR NR NR NR NA CSMD1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intron_variant chr8 4543602 rs11786902 0.6 NR NR NR NR NA CSMD1 SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intron_variant chr8 4543602 rs11786902 0.977 NR NR NR NR NA CSMD1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr8 4543602 rs11786902 1 NR NR NR 1.01 1.01 CSMD1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr8 9141509 rs3748140 0.000000305 PPP1R3B NR NR 2.43 2.43 PPP1R3B SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD missense_variant chr8 9141509 rs3748140 0.00000493 PPP1R3B NR NR NR NA PPP1R3B SNP-based Disease risk 22832961 Caucasian ADGC 8292 All LOAD AD missense_variant chr8 9141509 rs3748140 0.000575 PPP1R3B NR NR 2.8 2.8 PPP1R3B SNP-based Disease risk 22832961 Caucasian ADGC 2229 All LOAD AD missense_variant chr8 9141509 rs3748140 0.00657 PPP1R3B NR NR 3.47 3.47 PPP1R3B SNP-based Disease risk 22832961 Caucasian ADGC 2099 All LOAD AD missense_variant chr8 9141509 rs3748140 0.0148 PPP1R3B NR NR 2.24 2.24 PPP1R3B SNP-based Disease risk 22832961 Caucasian ADGC 2321 All LOAD AD missense_variant chr8 9141509 rs3748140 0.131 PPP1R3B NR NR 10.14 10.14 PPP1R3B SNP-based Disease risk 22832961 Caucasian ADNI 381 All LOAD AD missense_variant chr8 9141509 rs3748140 0.182 PPP1R3B NR NR 1.62 1.62 PPP1R3B SNP-based Disease risk 22832961 Caucasian MIRAGE 1262 All LOAD AD missense_variant chr8 9400343 rs117922969 0.000531 AK055863 T T NR NA TNKS SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr8 9400343 rs117922969 0.00143 AK055863 T T NR NA TNKS SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr8 9400343 rs117922969 0.598 AK055863 T T 1 1 TNKS SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr8 9933227 rs17150816 0.000016 "MSRA, TNKS" NR NR NR NA MSRA SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD upstream_gene_variant chr8 10477271 rs11782819 0.191 UNQ9391 NR NR NR NA PRSS51 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology non_coding_transcript_exon_variant chr8 10477271 rs11782819 0.428 UNQ9391 NR NR NR NA PRSS51 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology non_coding_transcript_exon_variant chr8 10784455 rs7014168 0.000139 SOX7 A A 0.94 0.94 PINX1 SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr8 10784455 rs7014168 0.000357 SOX7 A A 0.95 0.95 PINX1 SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr8 10784455 rs7014168 0.000401 SOX7 A A NR NA PINX1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr8 10784455 rs7014168 0.000428 SOX7 A A NR NA PINX1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr8 10784455 rs7014168 0.0565 SOX7 A A 1 1 PINX1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr8 10784455 rs7014168 0.674 SOX7 A A 1.02 1.02 PINX1 SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr8 17639052 rs4921790 4.58E-09 "PDGFRL, MTUS1" C C 0.61 1.84043 PDGFRL SNP-based Endophenotype 29274321 Caucasian ADNI 268 Normal controls Hippocampal volume (HPV) Imaging intron_variant chr8 17727620 rs7842088 0.000000212 MTUS1 G G NR NA MTUS1 SNP-based Endophenotype 20932310 Caucasian ADNI 109 MCI CSF P-tau181p Fluid biomarker intron_variant chr8 20789812 rs55644114 2.54E-08 "GFRA2, LZTS1" A A 0.41 1.50682 LZTS1 SNP-based Endophenotype 29274321 Caucasian ADNI 730 All CSF Ab1-42 Fluid biomarker intergenic_region chr8 26915994 rs1481650 0.555 ADRA1A NR NR NR NA ADRA1A SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intergenic_region chr8 27298435 rs77389621 0.0584 TRIM35 NR NR 0.02716 1.02753 TRIM35 SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker intron_variant chr8 27313969 rs7833348 0.025 PTK2B A A 0.66 NA PTK2B SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr8 27337604 rs28834970 0.00000231 PIK2B NR NR 0.07 1.07251 PTK2B SNP-based eQTL 30448613 Caucasian ADNI 763 All TRIM35 (11723344_at) expression in blood Expression intron_variant chr8 27337604 rs28834970 0.0000043 PTK2B C C 1.11 1.11 PTK2B SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr8 27337604 rs28834970 0.046 PTK2B C C 1.13 1.13 PTK2B SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr8 27337604 rs28834970 0.23 PTK2B C C 1.09 1.09 PTK2B SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr8 27337604 rs28834970 0.27 PTK2B NR NR 1.1 1.1 PTK2B SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr8 27337604 rs28834970 0.571 PTK2B C C 0.975 0.975 PTK2B SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr8 27337604 rs28834970 1.18E-17 PIK2B NR NR 0.09 1.09417 PTK2B SNP-based eQTL 30448613 Caucasian ADNI 763 All PTK2B (11720982 s at) expression in blood Expression intron_variant chr8 27337604 rs28834970 3.30E-09 PTK2B C C 1.1 1.1 PTK2B SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr8 27337604 rs28834970 6.86E-18 PIK2B NR NR 0.11 1.11628 PTK2B SNP-based eQTL 30448613 Caucasian ADNI 763 All PTK2B (11720981_a_at) expression in blood Expression intron_variant chr8 27337604 rs28834970 7.33E-12 PIK2B NR NR 0.09 1.09417 PTK2B SNP-based eQTL 30448613 Caucasian ADNI 763 All PTK2B (11720980_a_at) expression in blood Expression intron_variant chr8 27337604 rs28834970 7.40E-14 PTK2B C C 1.1 1.1 PTK2B SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr8 27337604 rs28834970 NR PTK2B C C 1.22 1.22 PTK2B SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr8 27337604 rs28834970 NR ZCWPW1 C C 1.1 1.1 PTK2B SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr8 27337604 rs28834970 NR ZCWPW1 C C 1.38 1.38 PTK2B SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr8 27362470 rs73223431 0.000015 PTK2B T T 1.11 1.11 PTK2B SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr8 27362470 rs73223431 6.30E-14 PTK2B T T 1.1 1.1 PTK2B SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr8 27362470 rs73223431 8.30E-10 PTK2B T T 1.1 1.1 PTK2B SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr8 27373302 rs12679874 0.00000164 PTK2B A A NR NA PTK2B SNP-based Cross phenotype 27088644 Caucasian IGAP 54162 All AD AD intron_variant chr8 27373302 rs12679874 0.0000631 PTK2B NR NR -0.09 NA PTK2B SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr8 27373302 rs12679874 0.000438 PTK2B A A NR NA PTK2B SNP-based Cross phenotype 27088644 Caucasian Cohort of Immune-Mediated Diseases 51009 All Crohn disease Non-ADRD intron_variant chr8 27434232 rs12056620 0.0000756 PTK2B T T NR NA PTK2B SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr8 27434232 rs12056620 0.000335 PTK2B T T NR NA PTK2B SNP-based Cross phenotype 30413934 Caucasian GIANT 681275 All Body-mass index (BMI) Non-ADRD intron_variant chr8 27434232 rs12056620 0.00223 PTK2B T T 1.04 1.04 PTK2B SNP-based Disease risk 30413934 Caucasian "ADGC, IGAP" 79471 All AD AD intron_variant chr8 27434232 rs12056620 0.00266 PTK2B T T 1.04 1.04 PTK2B SNP-based Disease risk 30413934 Caucasian IGAP 74046 All AD AD intron_variant chr8 27434232 rs12056620 0.127 PTK2B T T 1 1 PTK2B SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr8 27434232 rs12056620 0.55 PTK2B T T 1.03 1.03 PTK2B SNP-based Disease risk 30413934 Caucasian ADGC 5425 All AD AD intron_variant chr8 27472579 rs2741342 0.00126 CHRNA2 NR NR 0.09 NA CHRNA2 SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr8 27545260 rs7341557 0.016 EPHX2 NR NR 0.02 1.0202 EPHX2 SNP-based Endophenotype 27933404 Caucasian "ADNI, BIOCARD, Knight-ADRC, Lund University, MAYO, UPENN, UW " 2886 AD subjects CSF Ab1-42 Fluid biomarker 3_prime_UTR_variant chr8 27565223 rs17466060 0.0000043 EPHX2 NR NR NR NA EPHX2 SNP-based Cross phenotype 28780673 Caucasian IGAP 54162 All AD AD intron_variant chr8 27565223 rs17466060 0.0005 EPHX2 NR NR NR NA EPHX2 SNP-based Cross phenotype 28780673 Caucasian "GAME-ON, IGAP" 116992 All AD + Breast cancer + Lung Cancer Non-ADRD intron_variant chr8 27565223 rs17466060 0.00057 EPHX2 NR NR NR NA EPHX2 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 28998 All Lung Cancer Non-ADRD intron_variant chr8 27565223 rs17466060 0.017 EPHX2 NR NR NR NA EPHX2 SNP-based Cross phenotype 28780673 Caucasian GAME-ON 33832 All Breast Cancer Non-ADRD intron_variant chr8 27571711 rs1316801 0.00000101 CLU NR NR NR NA CLU SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr8 27572989 rs7831810 0.01 CLU NR NR 0.09 NA CLU SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr8 27586760 rs881146 0.00213 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr8 27586760 rs881146 0.0374 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr8 27586760 rs881146 0.0617 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr8 27586760 rs881146 0.676 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr8 27589507 rs12680584 0.103 CLU A A 0.88 NA CLU SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other downstream_gene_variant chr8 27591212 rs7012010 0.0025 CLU C C 1.1 1.1 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD downstream_gene_variant chr8 27591212 rs7012010 0.0081 CLU C C 1.1 1.1 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD downstream_gene_variant chr8 27591212 rs7012010 0.043 CLU NR NR 1.1 1.1 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD downstream_gene_variant chr8 27591212 rs7012010 0.0469 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.0614 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.064 CLU NR NR 1.05 1.05 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD downstream_gene_variant chr8 27591212 rs7012010 0.0785 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.117 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.121 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.279 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.372 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.378 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.418 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.487 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.496 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.65 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.985 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD downstream_gene_variant chr8 27591212 rs7012010 0.99 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD downstream_gene_variant chr8 27595505 rs17057441 0.0177 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD downstream_gene_variant chr8 27595505 rs17057441 0.0452 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD downstream_gene_variant chr8 27595505 rs17057441 0.078 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD downstream_gene_variant chr8 27595505 rs17057441 0.677 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD downstream_gene_variant chr8 27597925 rs3087554 0.71 CLU C C 0.98 0.98 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD 3_prime_UTR_variant chr8 27597925 rs3087554 0.88 CLU NR NR 1.01 1.01 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD 3_prime_UTR_variant chr8 27597925 rs3087554 0.92 CLU C C 1 1 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD 3_prime_UTR_variant chr8 27597925 rs3087554 0.97 CLU NR NR 1 1 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD 3_prime_UTR_variant chr8 27598736 rs2279590 0.000001 CLU NR NR 0.83 0.83 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 7353 All AD AD intron_variant chr8 27598736 rs2279590 0.000019 CLU NR NR 0.81 0.81 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 4774 APOE-e4 carrier AD AD intron_variant chr8 27598736 rs2279590 0.00082 CLU NR NR 0.88 0.88 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 6900 All AD AD intron_variant chr8 27598736 rs2279590 0.00701 CLU T T 0.85 0.85 CLU SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr8 27598736 rs2279590 0.013 CLU NR NR 0.87 0.87 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 2616 All AD AD intron_variant chr8 27598736 rs2279590 0.013 CLU NR NR 0.92 0.92 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 9424 APOE-e4 non-carrier AD AD intron_variant chr8 27598736 rs2279590 0.031 CLU NR NR 0.82 0.82 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1576 All AD AD intron_variant chr8 27598736 rs2279590 0.034 CLU T T 1.41 1.41 CLU SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr8 27598736 rs2279590 0.036 "CLU,MIR6843" NR NR 0.01 1.01005 CLU SNP-based Endophenotype 30805717 Caucasian MAGIC 51750 All Fasting Insulin Fluid biomarker intron_variant chr8 27598736 rs2279590 0.097 CLU T T 0.82 0.82 CLU SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr8 27598736 rs2279590 0.24 CLU NR NR 0.91 0.91 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1544 All AD AD intron_variant chr8 27598736 rs2279590 0.35 CLU NR NR 0.92 0.92 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1232 All AD AD intron_variant chr8 27598736 rs2279590 3.75E-17 "CLU,MIR6843" NR NR -0.14 0.869358 CLU SNP-based Endophenotype 30805717 Caucasian IGAP 54162 All AD AD intron_variant chr8 27598736 rs2279590 8.90E-09 CLU NR NR 0.86 0.86 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 14253 All AD AD intron_variant chr8 27603578 rs9331926 0.02 CLU G G 1.96 1.96 CLU SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr8 27604964 rs7982 0.0002 CLU T T 0.87 0.87 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD synonymous_variant chr8 27604964 rs7982 0.000364 CLU NR NR 0.91 0.91 CLU SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD synonymous_variant chr8 27604964 rs7982 0.0046 CLU T T 0.89 0.89 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD synonymous_variant chr8 27604964 rs7982 0.0092 CLU NR NR 0.87 0.87 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD synonymous_variant chr8 27604964 rs7982 0.22 CLU NR NR 0.92 0.92 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD synonymous_variant chr8 27607002 rs11136000 0.000000523 CLU A A 0.89 0.89 CLU SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD intron_variant chr8 27607002 rs11136000 0.0000015 CLU NR NR 0.83 0.83 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 7282 All AD AD intron_variant chr8 27607002 rs11136000 0.000027 CLU NR NR 0.81 0.81 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 4760 APOE-e4 carrier AD AD intron_variant chr8 27607002 rs11136000 0.000498 CLU T T 0.89 0.89 CLU SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE" 16675 All AD AD intron_variant chr8 27607002 rs11136000 0.0007 CLU T T 0.91 0.91 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr8 27607002 rs11136000 0.000781 CLU A A 0.17 1.1853 CLU SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data CLU (ILMN_1667058) expression in Temporal cortex (TCX) Expression intron_variant chr8 27607002 rs11136000 0.00088 CLU NR NR 0.88 0.88 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 6929 All AD AD intron_variant chr8 27607002 rs11136000 0.0019 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr8 27607002 rs11136000 0.0029 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr8 27607002 rs11136000 0.007 CLU NR NR 0.91 0.91 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 9392 APOE-e4 non-carrier AD AD intron_variant chr8 27607002 rs11136000 0.0083 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr8 27607002 rs11136000 0.0096 CLU T T 0.92 0.92 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD intron_variant chr8 27607002 rs11136000 0.0096 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3461 Northwestern European ancestry LOAD AD intron_variant chr8 27607002 rs11136000 0.0108 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1877 Unrelated cases and controls subjects LOAD AD intron_variant chr8 27607002 rs11136000 0.0109 CLU T T 0.87 0.87 CLU SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr8 27607002 rs11136000 0.015 CLU NR NR 0.91 0.91 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD intron_variant chr8 27607002 rs11136000 0.0159 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr8 27607002 rs11136000 0.017 CLU NR NR 0.91 0.91 CLU SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 4363 All AD AD intron_variant chr8 27607002 rs11136000 0.022 CLU NR NR 0.8 0.8 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1454 All AD AD intron_variant chr8 27607002 rs11136000 0.0227 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3722 All LOAD AD intron_variant chr8 27607002 rs11136000 0.028 CLU NR NR 0.88 0.88 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 2695 All AD AD intron_variant chr8 27607002 rs11136000 0.03 CLU NR NR 0.82 0.82 CLU SNP-based Disease risk 20460622 Caucasian Cohort from Europe 2349 All AD AD intron_variant chr8 27607002 rs11136000 0.032 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 2167 APOE-e4+ LOAD AD intron_variant chr8 27607002 rs11136000 0.0361 CLU T T 0.79 0.79 CLU SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD intron_variant chr8 27607002 rs11136000 0.04 CLU T T 0.86 0.86 CLU SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr8 27607002 rs11136000 0.068 CLU A A 0.87 0.87 CLU SNP-based Disease risk 21390209 Caucasian ADGC 1525 All AD AD intron_variant chr8 27607002 rs11136000 0.088 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1642 APOE-e4/e3 LOAD AD intron_variant chr8 27607002 rs11136000 0.0956 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1672 APOE-e4- LOAD AD intron_variant chr8 27607002 rs11136000 0.11 CLU NR NR -0.018 0.982161 CLU SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Amygdala volume Imaging intron_variant chr8 27607002 rs11136000 0.122 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intron_variant chr8 27607002 rs11136000 0.153 CLU A A 0.93 0.93 CLU SNP-based Disease risk 21390209 Caucasian "ADNI, GenADA, Pfizer" 3595 All AD AD intron_variant chr8 27607002 rs11136000 0.17 CLU NR NR 0.93 0.93 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD intron_variant chr8 27607002 rs11136000 0.171 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3/e3 LOAD AD intron_variant chr8 27607002 rs11136000 0.24 CLU NR NR 0.91 0.91 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1544 All AD AD intron_variant chr8 27607002 rs11136000 0.243 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 250 APOE-e3/e2+e2/e2 LOAD AD intron_variant chr8 27607002 rs11136000 0.27 CLU NR NR 0.91 0.91 CLU SNP-based Endophenotype 26993346 Caucasian Cohort from Europe 10840 All PCA (posterior cortical atrophy) Imaging intron_variant chr8 27607002 rs11136000 0.31 CLU NR NR -0.03 0.970446 CLU SNP-based Endophenotype 20558387 Caucasian ADNI 740 All White matter lesion volume Imaging intron_variant chr8 27607002 rs11136000 0.31 CLU NR NR 0.92 0.92 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1236 All AD AD intron_variant chr8 27607002 rs11136000 0.373 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr8 27607002 rs11136000 0.488 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 3786 All LOAD AD intron_variant chr8 27607002 rs11136000 0.5 CLU NR NR -0.011 0.98906 CLU SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Temporal pole cortex thickness Imaging intron_variant chr8 27607002 rs11136000 0.582 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intron_variant chr8 27607002 rs11136000 0.65 CLU NR NR -0.011 0.98906 CLU SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Entorhinal cortex thickness Imaging intron_variant chr8 27607002 rs11136000 0.66 CLU NR NR 0.007 1.00702 CLU SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Parahippocampal gyrus cortex thickness Imaging intron_variant chr8 27607002 rs11136000 0.75 CLU NR NR 0.97 0.97 CLU SNP-based Disease risk 20558387 Caucasian ADNI 740 All AD + MCI AD intron_variant chr8 27607002 rs11136000 0.78 CLU NR NR -0.019 0.981179 CLU SNP-based Endophenotype 20558387 Caucasian ADNI 740 All Hippocampal volume Imaging intron_variant chr8 27607002 rs11136000 0.787 CLU A A 0.96 0.96 CLU SNP-based Disease risk 21390209 Caucasian ADNI 496 All AD AD intron_variant chr8 27607002 rs11136000 0.806 CLU A A 0.98 0.98 CLU SNP-based Disease risk 21390209 Caucasian GenADA 1574 All AD AD intron_variant chr8 27607002 rs11136000 0.951 CLU T T 1.01 1.01 CLU SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr8 27607002 rs11136000 0.962 CLU NR NR NR NA CLU SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intron_variant chr8 27607002 rs11136000 0.966 CLU NR NR NR NA CLU SNP-based Endophenotype 21390209 Caucasian "ADNI, leadC" 597 AD subjects AD Progression Cognitive intron_variant chr8 27607002 rs11136000 0.993 CUGBP2 NR NR NR NA CLU SNP-based Disease risk 21379329 Caucasian ADGC 408 APOE-e4/e4 LOAD AD intron_variant chr8 27607002 rs11136000 1.40E-09 CLU NR NR 0.84 0.84 CLU SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intron_variant chr8 27607002 rs11136000 1.49E-09 CLU T T 0.85 0.85 CLU SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI" 24035 All AD AD intron_variant chr8 27607002 rs11136000 1.62E-16 CLU T T 0.85 0.85 CLU SNP-based Disease risk 20460622 Caucasian "ADGC, CHARGE, EADI, GERAD" 34363 All AD AD intron_variant chr8 27607002 rs11136000 1.72E-16 CLU NR NR NR NA CLU SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr8 27607002 rs11136000 7.50E-09 CLU NR NR 0.86 0.86 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 14211 All AD AD intron_variant chr8 27607002 rs11136000 8.50E-10 CLU NR NR 0.86 0.86 CLU SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 19052 All AD AD intron_variant chr8 27607002 rs11136000 NS CLU A A 0.03 1.03045 CLU SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data CLU (ILMN_1667058) expression in Cerebellar tissue (CER) Expression intron_variant chr8 27607412 rs4236673 2.61E-19 "CLU, PTK2B" A A -8.98 NA CLU SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ, UKBB" 455258 All AD + AD-by-proxy AD intron_variant chr8 27607412 rs4236673 6.36E-20 "CLU, PTK2B" A A NR NA CLU SNP-based Disease risk 30617256 Caucasian "ADSP, IGAP, PGC-ALZ" 79145 All AD AD intron_variant chr8 27608664 rs1532277 5.01E-09 CLU NR NR 0.21 NA CLU SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other intron_variant chr8 27608798 rs1532278 0.0000202 CLU T T 0.89 0.89 CLU SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr8 27608798 rs1532278 0.0000555 CLU T T 0.9 0.9 CLU SNP-based Disease risk 21460841 Caucasian ADGC 15675 All LOAD AD intron_variant chr8 27608798 rs1532278 0.000256 CLU T T 0.87 0.87 CLU SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr8 27608798 rs1532278 0.000274 CLU T T 0.87 0.87 CLU SNP-based Disease risk 21460841 Caucasian ADGC 7096 All LOAD AD intron_variant chr8 27608798 rs1532278 0.661 CLU T T 0.05 1.05127 CLU SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr8 27608798 rs1532278 0.977 CLU T T 0 1 CLU SNP-based Age at onset (AAO) / Survival 25199842 Caucasian ADGC 9162 LOAD subjects Age of AD onset Other intron_variant chr8 27608798 rs1532278 0.992 NR T T 0 1 CLU SNP-based Endophenotype 23836404 Caucasian ADGC 725 All Neuritic Plaque Pathologic Burden Neuropathology intron_variant chr8 27608798 rs1532278 1.87E-08 CLU T T 0.89 0.89 CLU SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr8 27608798 rs1532278 7.45E-09 CLU/PTK2B A A NR NA CLU SNP-based Disease risk 30617256 Caucasian UKBB 376113 All AD-by-proxy AD intron_variant chr8 27608798 rs1532278 8.34E-08 CLU T T 0.89 0.89 CLU SNP-based Disease risk 21460841 Caucasian ADGC 22771 All LOAD AD intron_variant chr8 27610169 rs9331896 0.0000096 CLU C C 0.9 0.9 CLU SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 36569 APOE-e4- subjects AD AD intron_variant chr8 27610169 rs9331896 0.00015 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in intra-locular white matter (WHMT) Expression intron_variant chr8 27610169 rs9331896 0.00035 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in intra-locular white matter (WHMT) Expression intron_variant chr8 27610169 rs9331896 0.00045 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in temporal cortex (TCTX) Expression intron_variant chr8 27610169 rs9331896 0.00069 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in hippocampus (HIPP) Expression intron_variant chr8 27610169 rs9331896 0.00077 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in occipital cortex (OCTX) Expression intron_variant chr8 27610169 rs9331896 0.00102 CLU NR NR 0.92 0.92 CLU SNP-based Disease risk 30448613 Caucasian ADGC 15330 All AD AD intron_variant chr8 27610169 rs9331896 0.0012 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in frontal cortex (FCTX) Expression intron_variant chr8 27610169 rs9331896 0.0013 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in temporal cortex (TCTX) Expression intron_variant chr8 27610169 rs9331896 0.0015 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in hippocampus (HIPP) Expression intron_variant chr8 27610169 rs9331896 0.0047 CLU C C 0.84 0.84 CLU SNP-based Endophenotype 25188341 Caucasian ADGC 4914 All Clinico-pathologic AD dementia (No neuropathologist documentation) Neuropathology intron_variant chr8 27610169 rs9331896 0.03 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in substantia nigra (SNIG) Expression intron_variant chr8 27610169 rs9331896 0.04 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in frontal cortex (FCTX) Expression intron_variant chr8 27610169 rs9331896 0.042 CLU C C 0.85 0.85 CLU SNP-based Endophenotype 25188341 Caucasian ADGC 3702 All Clinico-pathologic AD dementia (with neuropathologist documentation) Neuropathology intron_variant chr8 27610169 rs9331896 0.07 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in occipital cortex (OCTX) Expression intron_variant chr8 27610169 rs9331896 0.08 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in cerebellar cortex (CRBL) Expression intron_variant chr8 27610169 rs9331896 0.14 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in substantia nigra (SNIG) Expression intron_variant chr8 27610169 rs9331896 0.14 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in thalamus (THAL) Expression intron_variant chr8 27610169 rs9331896 0.27 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in putamen (PUTM) Expression intron_variant chr8 27610169 rs9331896 0.5 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in medulla (MEDU) Expression intron_variant chr8 27610169 rs9331896 0.62 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in medulla (MEDU) Expression intron_variant chr8 27610169 rs9331896 0.69 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in thalamus (THAL) Expression intron_variant chr8 27610169 rs9331896 0.89 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (3129079) expression in cerebellar cortex (CRBL) Expression intron_variant chr8 27610169 rs9331896 0.94 CLU NR NR NR NA CLU SNP-based eQTL 26919393 Caucasian UKBEC 134 Healthy subjects CLU (t3129065) expression in putamen (PUTM) Expression intron_variant chr8 27610169 rs9331896 1.70E-09 CLU C C 0.87 0.87 CLU SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 18845 All Clinically diagnosed LOAD AD intron_variant chr8 27610169 rs9331896 2.80E-09 CLU C C 0.84 0.84 CLU SNP-based Disease risk 25778476 Caucasian "ADGC, IGAP" 21345 APOE-e4+ subjects AD AD intron_variant chr8 27610169 rs9331896 2.80E-25 CLU C C 0.86 0.86 CLU SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD, Cohorts from Europe and USA" 74046 All LOAD AD intron_variant chr8 27610169 rs9331896 3.60E-16 CLU C C 0.88 0.88 CLU SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 63926 All Clinically diagnosed LOAD AD intron_variant chr8 27610169 rs9331896 4.50E-10 CLU C C 0.86 0.86 CLU SNP-based Disease risk 24162737 Caucasian Cohorts from Europe and USA 19884 All LOAD AD intron_variant chr8 27610169 rs9331896 4.60E-24 CLU C C 0.88 0.88 CLU SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr8 27610169 rs9331896 9.60E-17 CLU C C 0.86 0.86 CLU SNP-based Disease risk 24162737 Caucasian "ADGC, CHARGE, EADI, GERAD" 54162 All LOAD AD intron_variant chr8 27610169 rs9331896 NR CLU T T 0.83 0.83 CLU SNP-based Disease risk 27849641 Caucasian ADGC 589 All Symptomatic AD (CDR global score >=0.5) AD intron_variant chr8 27610169 rs9331896 NR ZCWPW1 T T 0.73 0.73 CLU SNP-based Disease risk 27849641 Caucasian ADGC 297 APOE-e4 non-carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr8 27610169 rs9331896 NR ZCWPW1 T T 1.18 1.18 CLU SNP-based Disease risk 27849641 Caucasian ADGC 292 APOE-e4 carriers Symptomatic AD (CDR global score >=0.5) AD intron_variant chr8 27611345 rs9331888 0.000000094 CLU NR NR 1.16 1.16 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 14395 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.00000794 CLU NR NR 0.16 NA CLU SNP-based Age at onset (AAO) / Survival 28323831 Caucasian ADGC 15795 All Age of AD onset Other 5_prime_UTR_variant chr8 27611345 rs9331888 0.000018 CLU NR NR 1.19 1.19 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 7353 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.000078 CLU NR NR 1.21 1.21 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 4821 APOE-e4 carrier AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.0029 CLU NR NR 1.12 1.12 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 7042 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.0045 CLU NR NR 1.22 1.22 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 2715 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.018 CLU NR NR 1.09 1.09 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 9518 APOE-e4 non-carrier AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.0697 CLU G G 1.1 1.1 CLU SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.12 CLU NR NR 1.16 1.16 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1573 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.19 CLU NR NR 0.92 0.92 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4+ carrier AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.192 CLU G G 0.89 0.89 CLU SNP-based Disease risk 23565137 Asian Cohort from Korea 1468 All LOAD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.32 CLU NR NR 1.09 1.09 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1224 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.48 CLU NR NR 1.06 1.06 CLU SNP-based Disease risk 19734903 Caucasian Cohorts from Europe 1530 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.53 CLU NR NR 1.03 1.03 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 Subjects with APOE-e4- carrier AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.74 CLU G G 0.99 0.99 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 0.76 CLU G G 0.99 0.99 CLU SNP-based Disease risk 20697030 Caucasian ADGC 12969 All AD AD 5_prime_UTR_variant chr8 27611345 rs9331888 >9.90E-01 CLU G G 1 1 CLU SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD 5_prime_UTR_variant chr8 27622508 rs2582367 0.000000697 "CLU, SCARA3" NR NR NR NA CLU SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intergenic_region chr8 27630273 rs569214 0.00000198 CLU A A 0.24 1.27125 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data CLU (ILMN_1667058) expression in Temporal cortex (TCX) Expression upstream_gene_variant chr8 27630273 rs569214 0.0264 CLU A A 0.95 2.58571 SCARA3 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr8 27630273 rs569214 NS CLU A A -0.02 0.980199 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data CLU (ILMN_1667058) expression in Cerebellar tissue (CER) Expression upstream_gene_variant chr8 27637095 rs894019 0.000000009 CLU A A 0.28 1.32313 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data CLU (ILMN_1667058) expression in Temporal cortex (TCX) Expression intron_variant chr8 27637095 rs894019 NS CLU A A 0.01 1.01005 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data CLU (ILMN_1667058) expression in Cerebellar tissue (CER) Expression intron_variant chr8 27637095 rs894019 NS CLU A A 1 2.71828 SCARA3 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD intron_variant chr8 27648239 rs2582369 0.0000202 CLU A A 0.23 1.2586 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data CLU (ILMN_1667058) expression in Temporal cortex (TCX) Expression intron_variant chr8 27648239 rs2582369 NS CLU A A 0.07 1.07251 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data CLU (ILMN_1667058) expression in Cerebellar tissue (CER) Expression intron_variant chr8 27648239 rs2582369 NS CLU A A 1.04 2.82922 SCARA3 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD intron_variant chr8 27652913 rs570197 0.0000401 CLU G G 0.22 1.24608 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data CLU (ILMN_1667058) expression in Temporal cortex (TCX) Expression intron_variant chr8 27652913 rs570197 NS CLU G G 0.06 1.06184 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data CLU (ILMN_1667058) expression in Cerebellar tissue (CER) Expression intron_variant chr8 27652913 rs570197 NS CLU G G 0.97 2.63794 SCARA3 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD intron_variant chr8 27663228 rs542876 0.00000213 CLU A A 0.21 1.23368 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data CLU (ILMN_1667058) expression in Temporal cortex (TCX) Expression intron_variant chr8 27663228 rs542876 NS CLU A A -0.01 0.99005 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data CLU (ILMN_1667058) expression in Cerebellar tissue (CER) Expression intron_variant chr8 27679399 rs473024 0.0000104 CLU G G 0.24 1.27125 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 399 All subjects with Temporal Cortex data CLU (ILMN_1667058) expression in Temporal cortex (TCX) Expression upstream_gene_variant chr8 27679399 rs473024 NS CLU G G 0.06 1.06184 SCARA3 SNP-based eQTL 22722634 Caucasian MAYO 374 All subjects with Cerebellum data CLU (ILMN_1667058) expression in Cerebellar tissue (CER) Expression upstream_gene_variant chr8 27679399 rs473024 NS CLU G G 1.04 2.82922 SCARA3 SNP-based Disease risk 22722634 Caucasian ADGC 22771 All AD AD upstream_gene_variant chr8 27699009 rs4545046 0.00000712 LOC646843 NR NR NR NA SCARA3 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker upstream_gene_variant chr8 29184936 rs7007878 0.00000653 KIF13B A A 3.83 NA KIF13B SNP-based Disease risk 21379329 Caucasian ADGC 110 Southeastern European ancestry LOAD AD intron_variant chr8 37181847 rs1157242 0.000007 NR NR NR 1.17 1.17 KCNU1 SNP-based Disease risk 19734902 Caucasian Cohorts from Europe and USA 11789 All AD AD intergenic_region chr8 51826590 rs16916856 0.0000078 PCMTD1 C C NR NA PCMTD1 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr8 51826590 rs16916856 0.00069 PCMTD1 C C NR NA PCMTD1 SNP-based Disease risk 18823527 Caucasian MRC 2321 All LOAD AD intron_variant chr8 51826590 rs16916856 0.0036 PCMTD1 C C NR NA PCMTD1 SNP-based Disease risk 18823527 Caucasian MRC 3721 All LOAD AD intron_variant chr8 69517842 rs12548348 6.29E-11 SULF1 NR NR NR NA SULF1 SNP-based Endophenotype 27357110 Caucasian "ADNI, Knight-ADRC" 587 NA Plasma Prolactin Fluid biomarker intron_variant chr8 69517842 rs12548348 9.84E-26 SULF1 NR NR NR NA SULF1 SNP-based Cross phenotype 27357110 Caucasian "ADNI, Knight-ADRC" 543 NA CSF Prolactin Fluid biomarker intron_variant chr8 77365237 rs4637816 0.00000931 LOC102724874 NR NR NR NA PEX2 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intergenic_region chr8 80177631 rs7814569 0.00000118 "TPD52, ZBTB10" A A 0.51 NA TPD52 SNP-based Disease risk 21379329 Caucasian ADGC 1422 APOE-e3e3 LOAD AD intron_variant chr8 90639859 rs10102274 0.00000227 TMEM64 NR NR 0.85 2.33965 TMEM64 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intron_variant chr8 90639859 rs10102274 0.0000754 TMEM64 NR NR 1.05 2.85765 TMEM64 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intron_variant chr8 90639859 rs10102274 0.0066 TMEM64 NR NR 0.67 1.95424 TMEM64 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intron_variant chr8 94841480 rs11996455 0.00009 INTS8 NR NR NR NA INTS8 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr8 94948283 rs896854 0.0000052 TP53INP1 NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr8 94948283 rs896854 0.00416 TP53INP1 NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr8 94951776 rs524678 0.082 TP53INP1 A A 1.24 NA NDUFAF6 SNP-based Age at onset (AAO) / Survival 25649651 Caucasian ADGC 983 AD subjects AD Survival Other intron_variant chr8 94959693 rs2011566 0.000278 C80RF38 G G NR NA NDUFAF6 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr8 94959693 rs2011566 0.000383 C80RF38 G G NR NA NDUFAF6 SNP-based Cross phenotype 30413934 Caucasian CARDIoGRAMplusC4D 155197 All Coronary artery disease (CAD) Non-ADRD intron_variant chr8 94959693 rs2011566 0.00335 C80RF38 G G 1 1 NDUFAF6 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr8 94964023 rs4735340 0.000000092 NDUFAF6 A A 0.94 0.94 NDUFAF6 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 94437 All Clinically diagnosed LOAD AD intron_variant chr8 94964023 rs4735340 0.00000034 NDUFAF6 A A 0.94 0.94 NDUFAF6 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 82771 All Clinically diagnosed LOAD AD intron_variant chr8 94964023 rs4735340 0.097 NDUFAF6 A A 0.92 0.92 NDUFAF6 SNP-based Disease risk 30820047 Non-Hispanic Caucasian "ADGC, CHARGE, EADI, GERAD" 11666 All Clinically diagnosed LOAD AD intron_variant chr8 94968480 rs6982393 0.000039 "C8orf38, TP53INP1" NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr8 94968480 rs6982393 0.000311 "C8orf38, TP53INP1" NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr8 94988691 rs4734295 0.000068 "C8orf38, TP53INP1" NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr8 94988691 rs4734295 0.00014 "C8orf38, TP53INP1" NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr8 95038329 rs7812465 0.00021 C8orf38 NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr8 95038329 rs7812465 0.000333 C8orf38 NR NR NR NA NDUFAF6 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chr8 95041772 rs7818382 0.941 NDUFAF6 T T 1.003 1.003 NDUFAF6 SNP-based Disease risk 24495969 Caucasian Cohort from Spain 4372 All AD AD intron_variant chr8 95448461 rs3133780 0.00018 "C8orf37, LOC643228" NR NR NR NA C8orf37 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intron_variant chr8 97351848 rs16895579 0.0000089 TSPYL5 A A NR NA TSPYL5 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intergenic_region chr8 97351848 rs16895579 0.0000577 TSPYL5 A A NR NA TSPYL5 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intergenic_region chr8 97351848 rs16895579 0.108 TSPYL5 A A 1 1 TSPYL5 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intergenic_region chr8 100670549 rs1693575 0.00000324 SNX31 NR NR 0.36 1.43333 SNX31 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 673 All CSF Clusterin Fluid biomarker intergenic_region chr8 100670549 rs1693575 0.000463 SNX31 NR NR 0.44 1.55271 SNX31 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 270 Subjects with APOE-e4+ CSF Clusterin Fluid biomarker intergenic_region chr8 100670549 rs1693575 0.00148 SNX31 NR NR 0.33 1.39097 SNX31 SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 403 Subjects with APOE-e4- CSF Clusterin Fluid biomarker intergenic_region chr8 107074450 rs1461992 0.0000336 NR NR NR 0.49 0.49 ANGPT1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr8 107074450 rs1461992 0.000675 NR NR NR 0.56 0.56 ANGPT1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr8 107074450 rs1461992 0.00311 NR NR NR 0.51 0.51 ANGPT1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr8 107074450 rs1461992 0.179 NR NR NR 0.69 0.69 ANGPT1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr8 108601865 rs2928826 0.000000577 NR T T NR NA TMEM74 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intron_variant chr8 108617674 rs2935776 0.000000553 NR C C NR NA TMEM74 SNP-based Endophenotype 20932310 Caucasian ADNI 109 Normal controls CSF T-tau Fluid biomarker intron_variant chr8 115667320 rs13277568 0.00117 TRPS1 G G NR NA TRPS1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr8 115667320 rs13277568 0.00119 TRPS1 G G NR NA TRPS1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr8 115667320 rs13277568 0.261 TRPS1 G G 1 1 TRPS1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr8 117173494 rs11558471 8.70E-10 SLC30A8 NR NR NR NA SLC30A8 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD 3_prime_UTR_variant chr8 117525450 rs10111328 0.000379 MED30 T T NR NA MED30 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intron_variant chr8 117525450 rs10111328 1.67E-20 NR T T NR NA MED30 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) MED30 (ILMN_1671603) expression in peripheral blood Expression intron_variant chr8 121897448 rs956225 0.00000871 NR G G 0.3 0.3 HAS2 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD intron_variant chr8 122973468 rs3802266 1.93E-95 ZHX2 NR NR -1.94 0.143704 ZHX2 SNP-based eQTL 22685416 Caucasian MAYO 374 All ZHX2 expression in Cerebellar Expression 3_prime_UTR_variant chr8 122973468 rs3802266 2.97E-101 ZHX2 NR NR -2.35 0.0953692 ZHX2 SNP-based eQTL 22685416 Caucasian MAYO 399 All ZHX2 expression in Temporal cortex Expression 3_prime_UTR_variant chr8 122973468 rs3802266 3.63E-38 ZHX2 NR NR -1.89 0.151072 ZHX2 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD ZHX2 expression in Cerebellar Expression 3_prime_UTR_variant chr8 122973468 rs3802266 9.47E-51 ZHX2 NR NR -1.99 0.136695 ZHX2 SNP-based eQTL 22685416 Caucasian MAYO 197 AD ZHX2 expression in Cerebellar Expression 3_prime_UTR_variant chr8 124272118 rs4457311 0.336 LOC442396 NR NR NR NA TMEM65 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology intron_variant chr8 124300419 rs10956170 0.912 TMEM65 NR NR NR NA TMEM65 SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology upstream_gene_variant chr8 130734543 rs726411 0.000245 ADCY8 G G 0.62 0.62 ADCY8 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intergenic_region chr8 132399360 rs2673604 0.0000026 KCNQ3 A A NR NA KCNQ3 SNP-based Disease risk 21379329 Caucasian ADGC 3839 All LOAD AD intron_variant chr8 143203248 rs4075205 0.0000366 NP_835466.1 NR NR NR NA GPIHBP1 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intergenic_region chr8 143538865 rs3750208 0.00000728 ZC3H3 A A 0.37 0.37 ZC3H3 SNP-based Disease risk 22159054 African American ADGC 1009 All LOAD AD missense_variant chr9 1521204 rs9886784 0.000312 NR A A 3.23 3.23 SMARCA2 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1410 All AD AD intergenic_region chr9 1521204 rs9886784 0.0429 NR A A 2.9 2.9 SMARCA2 SNP-based Disease risk 17998437 Caucasian MRC 639 All AD AD intergenic_region chr9 2742771 rs2034764 0.00000382 "KCNV2, VLDLR" NR NR NR NA PUM3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr9 2742771 rs2034764 0.00000434 "KCNV2, VLDLR" NR NR NR NA PUM3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 2222 AD subjects Age at onset Other intron_variant chr9 2742771 rs2034764 0.00111 "KCNV2, VLDLR" NR NR 0.88 2.4109 PUM3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 1190 AD subjects Age at onset Other intron_variant chr9 2742771 rs2034764 0.00162 "KCNV2, VLDLR" NR NR 0.76 2.13828 PUM3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADGC 844 AD subjects Age at onset Other intron_variant chr9 2742771 rs2034764 0.236 "KCNV2, VLDLR" NR NR 2.52 12.4286 PUM3 SNP-based Age at onset (AAO) / Survival 22005931 Caucasian ADNI 188 AD subjects Age at onset Other intron_variant chr9 2828765 rs2173904 0.019 KIAA0020 NR NR 1.45 1.45 PUM3 SNP-based Cross phenotype 30010129 Asian Cohort from Han Chinse 475 All AD AD missense_variant chr9 2833267 rs10217194 0.00709 KIAA0020 NR NR NR NA PUM3 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr9 2833267 rs10217194 0.05889 NA NR NR NR NA PUM3 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr9 3388125 rs62526377 0.00487 RFX3 NR NR NR NA RFX3 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr9 3388125 rs62526377 0.16583 NA NR NR NR NA RFX3 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr9 3927704 rs622536 0.000000045 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr9 3927704 rs622536 0.000000668 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr9 3927704 rs622536 0.029 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr9 3927841 rs623295 0.000000045 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr9 3927841 rs623295 0.000000668 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr9 3927841 rs623295 0.00466 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr9 3928115 rs624290 0.000000045 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr9 3928115 rs624290 0.000000668 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr9 3928115 rs624290 0.00466 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr9 3929424 rs514716 0.00000002 NR NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr9 3929424 rs514716 0.00000023 NR NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr9 3929424 rs514716 0.000000414 NR NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr9 3929424 rs514716 0.000000743 NR NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr9 3929424 rs514716 0.00000136 GLIS1 C C 0.044 1.04498 GLIS3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF T-tau Fluid biomarker intron_variant chr9 3929424 rs514716 0.0000345 GLIS1 NR NR 0.05 1.05127 GLIS3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1509 Female subjects CSF P-tau181p Fluid biomarker intron_variant chr9 3929424 rs514716 0.0004 GLIS1 NR NR 0.04 1.04081 GLIS3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1527 Male subjects CSF P-tau181p Fluid biomarker intron_variant chr9 3929424 rs514716 0.0145 GLIS1 C C 0.045 1.04603 GLIS3 SNP-based Age at onset (AAO) / Survival 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 39855 AD subjects Age at onset Other intron_variant chr9 3929424 rs514716 0.026 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF Ab1-42 Fluid biomarker intron_variant chr9 3929424 rs514716 0.0505 GLIS1 C C 0.95 2.58571 GLIS3 SNP-based Disease risk 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 74046 All AD risk AD intron_variant chr9 3929424 rs514716 0.294 GLIS1 C C 0.01 1.01005 GLIS3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF Ab1-42 Fluid biomarker intron_variant chr9 3929424 rs514716 0.36 NR G G -0.036 0.96464 GLIS3 SNP-based Neuropathology 23562540 NR ROSMAP 651 All tangle counts Neuropathology intron_variant chr9 3929424 rs514716 0.479 NR G G 0.004 1.00401 GLIS3 SNP-based Cognitive 23562540 NR ROSMAP 1593 All global cognitive decline Cognitive intron_variant chr9 3929424 rs514716 0.518 NR G G -0.022 0.97824 GLIS3 SNP-based Disease risk 23562540 Caucasian ADGC 22771 All AD AD intron_variant chr9 3929424 rs514716 0.666 GLIS1 C C 0.029 1.02942 GLIS3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 1530 All AD Progression (based on CDR Score) Cognitive intron_variant chr9 3929424 rs514716 1.07E-08 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr9 3929424 rs514716 1.38E-08 NR NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF T-tau Fluid biomarker intron_variant chr9 3929424 rs514716 2.94E-08 GLIS1 C C 0.049 1.05022 GLIS3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3146 All CSF P-tau181p Fluid biomarker intron_variant chr9 3929424 rs514716 2.94E-08 GLIS1 NR NR 0.05 1.05127 GLIS3 SNP-based Endophenotype 28247064 Caucasian "ADNI, BIOCARD, HB, Knight-ADRC, MAYO, SWEDEN, UPENN, UW" 3036 All CSF P-tau181p Fluid biomarker intron_variant chr9 3929424 rs514716 3.22E-09 GLIS3 NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr9 3929424 rs514716 3.76E-08 NR NR NR NR NA GLIS3 SNP-based Endophenotype 23562540 Caucasian "ADNI, Knight-ADRC, UPENN, UW" 1269 All CSF P-tau181p Fluid biomarker intron_variant chr9 6248035 rs11792633 0.928 IL33 T T 0.99 0.99 IL33 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr9 8095638 rs6477258 0.00000719 NR NR NR NR NA DMAC1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr9 8095638 rs6477258 0.000173 NR NR NR 1.51 1.51 DMAC1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr9 8095638 rs6477258 0.00114 NR NR NR NR NA DMAC1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr9 8095638 rs6477258 0.0025 NR NR NR NR NA DMAC1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr9 8095638 rs6477258 0.0255 NR NR NR 1.74 1.74 DMAC1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr9 8095638 rs6477258 0.051 NR NR NR 1.4 1.4 DMAC1 SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr9 8095638 rs6477258 NA NR NR NR NR NA DMAC1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr9 8095638 rs6477258 NA NR NR NR NR NA DMAC1 SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr9 8125410 rs10758939 0.00000475 NR NR NR NR NA PTPRD SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr9 8125410 rs10758939 0.000124 NR NR NR 0.67 0.67 PTPRD SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 1093 All LOAD AD intergenic_region chr9 8125410 rs10758939 0.000478 NR NR NR NR NA PTPRD SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr9 8125410 rs10758939 0.00421 NR NR NR NR NA PTPRD SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr9 8125410 rs10758939 0.00976 NR NR NR 0.69 0.69 PTPRD SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 894 APOE-e4- LOAD AD intergenic_region chr9 8125410 rs10758939 0.0877 NR NR NR 0.64 0.64 PTPRD SNP-based Disease risk 21059989 Caribbean Hispanic "EFIGA, WHICAP" 199 APOE-e4+ LOAD AD intergenic_region chr9 8125410 rs10758939 0.25155 NR NR NR NR NA PTPRD SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr9 8125410 rs10758939 0.3656 NR NR NR NR NA PTPRD SNP-based Disease risk 21059989 Caucasian ADGC 2449 Family-based individuals LOAD AD intergenic_region chr9 8125410 rs10758939 0.689 NR NR NR NR NA PTPRD SNP-based Disease risk 21059989 Caucasian ADGC 1390 Unrelated individuals LOAD AD intergenic_region chr9 10395255 rs11793419 0.00000533 PTPRD NR NR NR NA PTPRD SNP-based Endophenotype 26545630 Caucasian "ADNI, Knight-ADRC" 818 All Plasma Clusterin Fluid biomarker intron_variant chr9 16161235 rs4961664 0.00000444 C9orf92 T T 0.81 0.81 C9orf92 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD intergenic_region chr9 16231987 rs9407730 0.00000361 NR G G -0.21 0.810584 C9orf92 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intron_variant chr9 20145990 rs2039461 0.0000348 NR NR NR NR NA MLLT3 SNP-based Disease risk 19118814 Caucasian CAP 988 All LOAD AD intergenic_region chr9 27543283 rs3849942 0.0048 C9orf72 NR NR NR NA C9orf72 SNP-based Cross phenotype 29630712 Caucasian UKBEC NR All MOBKL2B expression in brain Expression downstream_gene_variant chr9 27543283 rs3849942 6.29E-19 C9orf72 NR NR NR NA C9orf72 SNP-based Cross phenotype 29630712 Caucasian "ALS group, IGAP, FTGC, AFTD, PSP Genetics Consortium, IPDGC" 36052 All AD AD downstream_gene_variant chr9 27572636 rs2282240 0.000249 C9orf72 T T NR NA C9orf72 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intron_variant chr9 27572636 rs2282240 1.18E-90 NR T T NR NA C9orf72 SNP-based eQTL 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) C9orf72 (ILMN_1741881) expression Expression intron_variant chr9 27595997 rs13302855 0.00000404 C9orf72 NR NR NR NA C9orf72 SNP-based Cross phenotype 29630712 Caucasian "ALS group, IGAP, FTGC, AFTD, PSP Genetics Consortium, IPDGC" 36052 All AD AD intergenic_region chr9 27595997 rs13302855 0.013 C9orf72 NR NR NR NA C9orf72 SNP-based Cross phenotype 29630712 Caucasian UKBEC NR All LRRC19 expression in brain Expression intergenic_region chr9 28414341 rs10968576 0.253 NR G G 1.03 1.03 LINGO2 SNP-based Cross phenotype 26079416 Caucasian ADGC 19692 All AD AD intron_variant chr9 28414341 rs10968576 0.731 NR G G 0 1 LINGO2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Memory function (PMID:22992720; Documentation of Cognitive Functioning Measures in the Health and Retirement Study) Cognitive intron_variant chr9 28414341 rs10968576 0.817 NR G G 1.01 1.01 LINGO2 SNP-based Cross phenotype 26079416 Caucasian GERAD 10454 All AD AD intron_variant chr9 28414341 rs10968576 0.921 NR G G 1 1 LINGO2 SNP-based Cross phenotype 26079416 Caucasian HRS 8403 All Dementia probability score (PMID:22992720) AD intron_variant chr9 28753984 rs10968750 0.00000197 LINGO2 T T 2.63 2.63 LINGO2 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intergenic_region chr9 31546474 rs4576506 0.00000104 RP11-291J9.2 NR NR 1.66 1.66 ACO1 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD, Cohort from UK" 7693 AD+P and control subjects AD+Psychosis ADRD intergenic_region chr9 35722285 rs2295797 0.00124 TPM2 C C NR NA TLN1 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD intron_variant chr9 35722285 rs2295797 3.22E-144 NR C C NR NA TLN1 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group TPM2 (ILMN_1757604) expression Expression intron_variant chr9 35722285 rs2295797 6.45E-181 NR C C NR NA TLN1 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group TPM2 (ILMN_1789196) expression Expression intron_variant chr9 35960467 rs12378268 0.00000543 OR2S2 NR NR 1.14 1.14 OR2S2 SNP-based Disease risk 30979435 Caucasian ADGC 14185 Age 60-79 y AD AD upstream_gene_variant chr9 35960467 rs12378268 0.363 OR2S2 NR NR 1.04 1.04 OR2S2 SNP-based Disease risk 30979435 Caucasian ADGC 6339 Age >=80 y AD AD upstream_gene_variant chr9 36972798 rs138898773 0.008 PAX5 NR NR NR NA PAX5 SNP-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr9 36972798 rs138898773 0.4016 NA NR NR NR NA PAX5 Gene-based Cross phenotype 30010129 Caucasian IGAP 54162 All AD AD intron_variant chr9 37036250 rs2282079 0.00000381 PAX5 G G 0.6 0.6 PAX5 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 17480 Plan 1 (males and females) AD AD upstream_gene_variant chr9 38189530 rs894520 0.936 NR NR NR NR NA SHB SNP-based Endophenotype 20452100 Caucasian ADGC 311 Non-Demented autopsy subjects High Braak vs Low Braak Neuropathology upstream_gene_variant chr9 71684384 rs7858861 0.0141 TMEM2 G G NR NA CEMIP2 SNP-based Disease risk 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group AD AD 3_prime_UTR_variant chr9 71684384 rs7858861 1.78E-15 NR G G NR NA CEMIP2 SNP-based eQTL 31055733 Caucasian "ADGC, CHS, CHARGE, HRS" 4806 HTN-N group TMEM2 (ILMN_1784661) expression Expression 3_prime_UTR_variant chr9 75999104 rs11144711 0.000565 PCSK5 G G NR NA PCSK5 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr9 75999104 rs11144711 0.00249 PCSK5 G G NR NA PCSK5 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD intron_variant chr9 75999104 rs11144711 0.855 PCSK5 G G 1 1 PCSK5 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr9 79282450 rs17198915 0.0000036 "CHCHD9, KRT18P24" NR NR NR NA TLE4 SNP-based Cross phenotype 28870582 Caucasian DIAGRAM 69033 All Type 2 diabetes (T2D) Non-ADRD intergenic_region chr9 83599234 rs12339683 0.000311 IDNK T T NR NA IDNK SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Low-density lipoprotein (LDL) Non-ADRD upstream_gene_variant chr9 83599234 rs12339683 0.00131 IDNK T T NR NA IDNK SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr9 83599234 rs12339683 0.00306 IDNK T T 1.01 1.01 IDNK SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD upstream_gene_variant chr9 86078545 rs7019241 0.000292 GOLPH2 T T 0.54 0.54 GOLM1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1214 All AD AD intron_variant chr9 86078545 rs7019241 0.00982 GOLPH2 T T 0.51 0.51 GOLM1 SNP-based Disease risk 17998437 Caucasian MRC 538 All AD AD intron_variant chr9 86085145 rs10868366 0.000243 GOLPH2 T T 0.55 0.55 GOLM1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1380 All AD AD intron_variant chr9 86085145 rs10868366 0.00122 GOLPH2 T T 0.46 0.46 GOLM1 SNP-based Disease risk 17998437 Caucasian MRC 641 All AD AD intron_variant chr9 87110354 rs7856774 0.0000549 NR NR NR 3.52 3.52 GAS1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr9 87110354 rs7856774 0.0000559 NR NR NR 2.15 2.15 GAS1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr9 87110354 rs7856774 0.0002 NR NR NR 2.13 2.13 GAS1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intergenic_region chr9 87110354 rs7856774 0.00832 NR NR NR 1.88 1.88 GAS1 SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intergenic_region chr9 87530200 rs12378187 0.02 DAPK1 G G 0.79 0.79 DAPK1 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1341 All Age of AD onset Other intron_variant chr9 87530200 rs12378187 0.29 DAPK1 G G 0.86 0.86 DAPK1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1341 All AD AD intron_variant chr9 87578076 rs4878104 0.334 DAPK1 T T 1.08 1.08 DAPK1 SNP-based Disease risk 20534741 Caucasian "ADC, UM" 1610 All AD AD intron_variant chr9 90726252 rs1172922 0.00000456 SYK A A 1.41 1.41 SYK SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 10191 Plan 3 (only females) AD AD intergenic_region chr9 103261938 rs16922670 0.00000722 RP11-341A22.2 NR NR 1.63 1.63 CYLC2 SNP-based Disease risk 22005930 Caucasian "ADGC, GERAD" 2034 AD+P and AD-P subjects AD+Psychosis ADRD intron_variant chr9 104868152 rs10991386 0.000000619 ABCA1 G G NR NA ABCA1 SNP-based Cross phenotype 30413934 Caucasian ENGAGE 62166 All Total cholesterol (TC) Non-ADRD intron_variant chr9 104868152 rs10991386 0.0000854 ABCA1 G G NR NA ABCA1 SNP-based Cross phenotype 30413934 Caucasian IGAP 54162 All AD AD intron_variant chr9 104868152 rs10991386 0.0233 ABCA1 G G 1 1 ABCA1 SNP-based Disease risk 30413934 Caucasian UKBB 376113 All AD AD intron_variant chr9 109849099 rs913360 0.000000183 PALM2 G G 1.56 1.56 PALM2AKAP2 SNP-based Disease risk 23565137 Asian Cohort from Japan 2024 All LOAD AD intron_variant chr9 109849099 rs913360 0.0000066 PALM2 G G 1.29 1.29 PALM2AKAP2 SNP-based Disease risk 23565137 Asian Cohort from Japan 3894 All LOAD AD intron_variant chr9 109849099 rs913360 0.16 PALM2 G G 1.11 1.11 PALM2AKAP2 SNP-based Disease risk 23565137 Asian Cohort from Japan 1870 All LOAD AD intron_variant chr9 118689608 rs1360806 0.0000401 DBC1 NR NR NR NA BRINP1 SNP-based Disease risk 20061627 Caucasian ADGC 699 All LOAD AD intron_variant chr9 118708097 rs10984186 0.000000423 CDK5RAP2 NR NR 1.43 1.43 BRINP1 SNP-based Disease risk 29360470 Caucasian Cohort from Quebec Founder Population 1943 All AD AD upstream_gene_variant chr9 118708097 rs10984186 0.013 CDK5RAP2 NR NR NR NA BRINP1 SNP-based Endophenotype 29360470 Caucasian ADNI 541 All Hippocampal volume Neuropathology upstream_gene_variant chr9 118708097 rs10984186 0.016 CDK5RAP2 NR NR NR NA BRINP1 SNP-based Endophenotype 29360470 Caucasian Cohort from Quebec Founder Population 141 All Neurofibrillary tangle (NFT) density Neuropathology upstream_gene_variant chr9 118708097 rs10984186 0.0462 CDK5RAP2 NR NR 1.35 1.35 BRINP1 SNP-based Disease risk 29360470 Caucasian ADNI 535 All AD AD upstream_gene_variant chr9 118708097 rs10984186 0.225 CDK5RAP2 NR NR NR NA BRINP1 SNP-based Disease risk 29360470 Caucasian IGAP 54162 All AD AD upstream_gene_variant chr9 122388609 rs12551233 0.000000479 PTGS1 G G -0.32 0.726149 PTGS1 SNP-based Endophenotype 23836404 Caucasian ADGC 651 All Neuritic plaque (NP) Neuropathology intron_variant chr9 126594025 rs144621483 0.000000043 NR T T -1.77 0.170333 LMX1B SNP-based Endophenotype 25188341 Caucasian ADGC 4046 All Neuritic Plaque Neuropathology intron_variant chr9 130135914 rs2240913 1.23E-63 GPR107 NR NR 0.66 1.93479 GPR107 SNP-based eQTL 22685416 Caucasian MAYO 374 All GPR107 expression in Cerebellar Expression 3_prime_UTR_variant chr9 130135914 rs2240913 1.66E-30 GPR107 NR NR 0.69 1.99372 GPR107 SNP-based eQTL 22685416 Caucasian MAYO 197 AD GPR107 expression in Cerebellar Expression 3_prime_UTR_variant chr9 130135914 rs2240913 1.84E-28 GPR107 NR NR 0.62 1.85893 GPR107 SNP-based eQTL 22685416 Caucasian MAYO 177 Non-AD GPR107 expression in Cerebellar Expression 3_prime_UTR_variant chr9 130135914 rs2240913 5.66E-77 GPR107 NR NR 0.95 2.58571 GPR107 SNP-based eQTL 22685416 Caucasian MAYO 399 All GPR107 expression in Temporal cortex Expression 3_prime_UTR_variant chr9 131513059 rs7865761 0.04 POMT1 G G 1.53 1.53 POMT1 SNP-based Disease risk 17998437 Caucasian Cohorts from Canada 1368 All AD AD intron_variant chr9 131513059 rs7865761 0.78 POMT1 G G 1.03 1.03 POMT1 SNP-based Age at onset (AAO) / Survival 17998437 Caucasian Cohorts from Canada 1368 All Age of AD onset Other intron_variant chr9 133038965 rs689266 0.000015 GTF3C5 NR NR NR NA GTF3C5 SNP-based Cross phenotype 28870582 Caucasian IGAP 54162 All AD AD intron_variant chrX 9835504 rs2405940 0.0003 SHROOM2 NR NR NR NA SHROOM2 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chrX 43732253 rs5905859 0.000019 MAOA NR NR 2.27 2.27 MAOA SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intron_variant chrX 43732253 rs5905859 0.059 MAOA NR NR 1.44 1.44 MAOA SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intron_variant chrX 43732253 rs5905859 0.152 NR NR NR 1.45 1.45 MAOA SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 235 All women LOAD AD intron_variant chrX 43732253 rs5905859 0.376 NR NR NR 1.21 1.21 MAOA SNP-based Disease risk 22785395 Caucasian Cohort fro Polish 282 All women LOAD AD intron_variant chrX 46465158 rs7876304 0.0009 ZNF673 NR NR NR NA KRBOX4 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chrX 46607340 rs1883255 0.0015 SLC9A7 NR NR NR NA SLC9A7 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chrX 74448994 rs479640 0.0038 SLC16A2 NR NR NR NA SLC16A2 SNP-based Endophenotype 22245343 Caucasian ADNI 757 All MRI Imaging intron_variant chrX 87181248 rs5969117 0.00000142 KLHL4 C C 1.49 1.49 KLHL4 SNP-based Disease risk 30636644 Caucasian "ADGC, CHS, CHARGE, HRS" 7289 Plan 2 (only males) AD AD intergenic_region chrX 92138738 rs5984894 0.0000002 PCDH11X NR NR 1.75 1.75 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.00000022 PCDH11X NR NR 1.3 1.3 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 80+ years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.0000048 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 All LOAD AD intron_variant chrX 92138738 rs5984894 0.000015 PCDH11X NR NR 1.39 1.39 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 60-80 years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.000057 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 All LOAD AD intron_variant chrX 92138738 rs5984894 0.0001 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 All LOAD AD intron_variant chrX 92138738 rs5984894 0.0002 PCDH11X NR NR 1.7 1.7 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.0002 PCDH11X NR NR 1.92 1.92 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.001 PCDH11X NR NR 1.45 1.45 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 80+ years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.001 PCDH11X NR NR 2.28 2.28 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.002 PCDH11X NR NR 1.23 1.23 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 80+ years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.006 PCDH11X NR NR 1.4 1.4 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 60-80 years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.01 PCDH11X NR NR 1.26 1.26 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.01 PCDH11X NR NR 1.35 1.35 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 60-80 years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.01 PCDH11X NR NR 1.96 1.96 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.02 PCDH11X NR NR 1.43 1.43 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.02 PCDH11X NR NR 1.44 1.44 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 60-80 years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.02 PCDH11X NR NR 2.02 2.02 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.03 PCDH11X NR NR 1.66 1.66 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.03 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 All LOAD AD intron_variant chrX 92138738 rs5984894 0.04 PCDH11X NR NR 1.33 1.33 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.04 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 All LOAD AD intron_variant chrX 92138738 rs5984894 0.05 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 All LOAD AD intron_variant chrX 92138738 rs5984894 0.06 PCDH11X NR NR 1.71 1.71 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.07 PCDH11X NR NR 1.18 1.18 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.09 PCDH11X NR NR 2 2 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.09 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 All LOAD AD intron_variant chrX 92138738 rs5984894 0.1 PCDH11X NR NR 1.23 1.23 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 80+ years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.1 PCDH11X NR NR 1.58 1.58 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.15 PCDH11X NR NR 1.19 1.19 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.16 PCDH11X NR NR 1.46 1.46 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.19 PCDH11X NR NR 1.4 1.4 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.22 PCDH11X NR NR 1.55 1.55 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.31 PCDH11X NR NR 1.28 1.28 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.35 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 All LOAD AD intron_variant chrX 92138738 rs5984894 0.38 PCDH11X NR NR 1.33 1.33 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.43 PCDH11X NR NR 1.2 1.2 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.47 PCDH11X NR NR 0.76 0.76 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.47 PCDH11X NR NR 1.19 1.19 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.48 PCDH11X NR NR 1.19 1.19 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.5 PCDH11X NR NR 1.1 1.1 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 80+ years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.6 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 All LOAD AD intron_variant chrX 92138738 rs5984894 0.74 PCDH11X NR NR 1.04 1.04 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.83 PCDH11X NR NR 0.96 0.96 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 80+ years old subjects LOAD AD intron_variant chrX 92138738 rs5984894 0.86 PCDH11X NR NR 0.95 0.95 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.86 PCDH11X NR NR 1.04 1.04 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.89 PCDH11X NR NR 0.96 0.96 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.94 PCDH11X NR NR 0.97 0.97 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 0.95 PCDH11X NR NR 0.97 0.97 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92138738 rs5984894 3.90E-12 PCDH11X NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 All LOAD AD intron_variant chrX 92147221 rs2573905 0.00000016 NR NR NR 1.29 1.29 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 5010 All LOAD AD intron_variant chrX 92147221 rs2573905 0.0000039 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 All LOAD AD intron_variant chrX 92147221 rs2573905 0.000032 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 All LOAD AD intron_variant chrX 92147221 rs2573905 0.0001 NR NR NR 1.72 1.72 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 "Female Homozygotes, 60+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.0002 NR NR NR 1.68 1.68 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.0002 NR NR NR 1.85 1.85 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.00025 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 All LOAD AD intron_variant chrX 92147221 rs2573905 0.002 NR NR NR 2.16 2.16 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.009 NR NR NR 2.01 2.01 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.01 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 All LOAD AD intron_variant chrX 92147221 rs2573905 0.02 NR NR NR 2.48 2.48 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.03 NR NR NR 1.22 1.22 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 "Female Heterozygotes, 60+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.04 NR NR NR 1.3 1.3 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.05 NR NR NR 1.32 1.32 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2024 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.06 NR NR NR 1.69 1.69 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.06 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 All LOAD AD intron_variant chrX 92147221 rs2573905 0.07 NR NR NR 1.61 1.61 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 "Female Homozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.07 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 All LOAD AD intron_variant chrX 92147221 rs2573905 0.08 NR NR NR 1.17 1.17 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 "Male Hemizygotes, 60+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.08 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 All LOAD AD intron_variant chrX 92147221 rs2573905 0.09 NR NR NR 1.48 1.48 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.09 NR NR NR 1.6 1.6 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.11 NR NR NR 1.71 1.71 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.16 NR NR NR 1.39 1.39 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 447 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.17 NR NR NR 1.17 1.17 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.29 NR NR NR 1.41 1.41 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.33 NR NR NR 1.27 1.27 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 673 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.34 NR NR NR 1.22 1.22 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 "Male Hemizygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.35 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 All LOAD AD intron_variant chrX 92147221 rs2573905 0.47 NR NR NR 1.19 1.19 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.49 NR NR NR 1.17 1.17 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 904 "Female Heterozygotes, 60-80 years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.54 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 All LOAD AD intron_variant chrX 92147221 rs2573905 0.55 NR NR NR 0.8 0.8 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.55 NR NR NR 1.15 1.15 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.69 NR NR NR 1.05 1.05 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 2716 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.86 NR NR NR 1.06 1.06 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.88 NR NR NR 0.96 0.96 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 486 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.91 NR NR NR 0.97 0.97 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 906 "Male Hemizygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.94 NR NR NR 1.03 1.03 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 434 "Female Homozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 0.95 NR NR NR 1.01 1.01 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 890 "Female Heterozygotes, 80+ years old subjects" LOAD AD intron_variant chrX 92147221 rs2573905 5.40E-13 NR NR NR NR NA PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 4740 All LOAD AD intron_variant chrX 92176386 rs5941047 0.00008 NR NR NR 1.21 1.21 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 5037 All LOAD AD intron_variant chrX 92184068 rs4568761 0.001 NR NR NR 1.17 1.17 PCDH11X SNP-based Disease risk 19136949 Caucasian ADGC 5028 All LOAD AD intron_variant chrX 106034370 rs1804495 1.24E-12 SERPINA7 NR NR -0.11 0.895834 SERPINA7 SNP-based Endophenotype 23894628 Non-Hispanic Caucasian ADNI 521 All Plasma TBG Fluid biomarker missense_variant chrX 119393914 rs217969 0.5 NR T T 0.04 1.04081 SLC25A43 SNP-based Endophenotype 25027320 Caucasian Cohorts from Europe 515 AD subjects CSF P-tau181p Fluid biomarker upstream_gene_variant