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Table 3 List of 19 SNPs that were located at protein-binding sites and that have eQTLgene(s)

From: Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping

SNP Chromosome Base-pair position Genomic region Closest gene eQTL Enhancer Tissue Count eQTL Gene Count
rs4038131 2 17775032 intron VSNL1 not eQTL 12 1
rs75847378 2 40181517 intron SLC8A1-AS1 eQTL 6 1
rs4663105 2 127891427 intergenic BIN1 eQTL 5 1
rs6448799 4 11630049 intergenic HS3ST1 eQTL 19 1
rs11168036 5 139707439 downstream HBEGF not eQTL 61 5
rs185968827 6 56708510 intron DST eQTL 2 2
rs1476679 7 100004446 intron ZCWPW1 not eQTL 9 23
rs1532278 8 27466315 intron CLU eQTL 63 1
rs9331888 8 27468862 5′UTR CLU not eQTL 38 1
rs1582763 11 60021948 intergenic MS4A4A not eQTL 2 1
rs573521 11 102716980 upstream MMP3 not eQTL 5 1
rs249153 12 95324389 intergenic NDUFA12 not eQTL 1 1
rs56146971 14 91920101 downstream PPP4R3A not eQTL 11 1
rs7225151 17 5137047 intron LOC100130950 eQTL 2 9
rs111816999 17 6882443 intergenic ALOX12-AS1 not eQTL 1 2
rs117964204 17 48692082 intron CACNA1G not eQTL 10 1
rs4147929 19 1063443 intron ABCA7 eQTL 28 3
rs439401 19 45414451 intergenic APOE eQTL 102 2
rs7364180 22 42218856 intron CCDC134 not eQTL 64 25
  1. “eQTL” indicates whether the closest gene is eQTL gene or not. “Enhancer Tissue Count” indicates the number of tisseus or celll lines showed enhancer acitivity. “GWAS p-value” indicates p-value from GWAS Catalog database