Table 1 Genome-wide analysis of AD GWAS data implicates 14 candidate regulatory variants (outside chr19/APOE) with potential roles in brain tissue using the confluent context identification approach
From: Integrated genomic analysis and CRISPRi implicates EGFR in Alzheimer’s disease risk
From GWAS | Colocalization | Enhancers | TFBS | ||||||
|---|---|---|---|---|---|---|---|---|---|
Variant | rsID | Loci | Closest gene | Causal genes | Brain regions | ROADMAP | EpiMAP | HOMER | Motif logo |
chr1:161186243:C:A | rs11585858 | Not reported | ADAMTS4 | 2 | 3 | 6 | 32 | GLIS3 |
|
chr1:161189357:C:T | rs4233366 | Not reported | ADAMTS4 | 1 | 1 | 0 | 1 | PAX6 |
|
chr7:100242838:A:G | rs866500 | Not reported | PVRIG | 11 | 12 | 6 | 13 | GLIS3 |
|
chr7:100373690:T:C | rs2405442 | ZCWPW1/NYAP1 | PILRA | 7 | 10 | 2 | 8 | ERRA |
|
chr7:100374211:A:G | rs1859788 | ZCWPW1/NYAP1 | PILRA | 5 | 4 | 2 | 6 | ERRA |
|
chr7:100561944:A:G | rs2734897 | Not reported | AGFG2 | 12 | 12 | 0 | 1 | PPARE |
|
chr7:143410495:G:T | rs12703526 | EPHA1 | EPHA1 | 1 | 1 | 3 | 10 | SCL |
|
chr7:54881563:A:G | rs74504435 | SEC61G | SEC61G | 1 | 2 | 3 | 4 | OCT6 |
|
chr8:27354759:A:C | rs10109834 | PTK2B | PTK2B | 1 | 2 | 0 | 1 | NANOG |
|
chr16:31122128:C:T | rs1060506 | KAT8 | KAT8 | 1 | 1 | 0 | 1 | SMAD2 |
|
chr16:31143037:G:A | rs78924645 | Not reported | PRSS36 | 3 | 9 | 0 | 1 | C-MYC |
|
chr16:81739604:A:G | rs12444183 | PLCG2 | PLCG2 | 1 | 1 | 0 | 1 | TATA-BOX |
|
chr17:63492371:G:A | rs4351 | ACE | ACE | 3 | 5 | 0 | 1 | PRDM10 |
|
chr21:26161943:T:C | rs4817090 | APP | APP | 3 | 12 | 6 | 6 | CUX2 |
|
