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 |