Table 1:
Implicated target genes at 16 LOAD GWAS loci in microglial cells.
| GWAS_LOCUS | SENTINEL_SNP | PROXY_SNP | PROXY_SNP_POS_hg19 | R2 | TARGET_GENES | INT_NUMBER | INT_TYPE | CELL_TYPE |
|---|---|---|---|---|---|---|---|---|
| PLEKHA1 | rs7908662 | rs2421016 | chr10:124167512 | 0.99 | PLEKHA1, TCONS_00018622 | 1 | nearest | iMg |
| TSPAN14 | rs6586028 | rs9633740 | chr10:82265271 | 0.99 | TSPAN14, TCONS_00018255 | 2 | nearest and distal | iMg |
| BLNK | rs6584063 | rs117148433 | chr10:98017866 | 0.97 | BLNK, ZNF518A | 2 | nearest and distal | iMg |
| BLNK | rs6584063 | rs117699776 | chr10:98048265 | 0.87 | BLNK | 1 | distal | iMg |
| CELF1/SPI1 | rs10437655 | rs1377416 | chr11:47416746 | 0.97 | MIR4487 | 1 | nearest | iMg |
| MS4A | rs1582763 | rs10897011, rs11230180 | chr11:59961427 | 0.76 | MS4A6A | 1 | distal | iMg |
| MS4A | rs1582763 | rs718376 | chr11:60002935 | 0.77 | MS4A6A | 1 | distal | iMg |
| MS4A | rs1582763 | rs636317, rs636341 | chr11:60019150 | 0.84 | MS4A6A | 1 | distal | iMg |
| MS4A | rs1582763 | rs672399 | chr11:60020112 | 0.84 | MS4A6A | 1 | distal | iMg |
| TSPOAP1 | rs2632516 | rs2526377 | chr17:56410041 | 0.98 | MIR4736, BZRAP1-AS1 | 2 | nearest and distal | iMg |
| BIN1 | rs4663105 | rs34779859, rs6733839 | chr2:127892768 | 0.71 | BIN1 | 1 | nearest | iMg |
| CASS4 | rs6069737 | rs6064392 | chr20:54984768 | 0.91 | AURKA, CSTF1, RTFDC1, TCONS_00028450 | 2 | distal | iMg |
| CASS4 | rs6069737 | rs6024870 | chr20:54997568 | 0.97 | RTFDC1, TCONS_00028450 | 1 | distal | iMg, HMC3 |
| CASS4 | rs6069737 | rs544475179, rs7274581 | chr20:55018156 | 0.80 | CASS4 | 1 | nearest | iMg |
| APP | rs2154481 | rs469420 | chr21:27541944 | 0.71 | APP, AP000230.1 | 1 | nearest | iMg |
| SHARPIN | rs34173062 | rs34173062 | chr8:145158607 | 1.00 | GPAA1 | 1 | distal | iMg |
| PTK2B | rs73223431 | rs28834970 | chr8:27195121 | 0.99 | PTK2B | 1 | nearest | iMg |
| PTK2B | rs73223431 | rs755951 | chr8:27226790 | 0.80 | EPHX2 | 1 | distal | iMg |
| CLU | rs1532278 | rs2279590 | chr8:27456253 | 0.89 | PTK2B | 1 | distal | iMg |
| CLU | rs1532278 | rs1532277 | chr8:27466181 | 0.99 | PTK2B, TRIM35 | 1 | distal | iMg |
| CELF1/SPI1 | rs10437655 | rs11039225 | chr11:47430599 | 0.95 | PACSIN3, ACP2, NR1H3, MADD, MIR4487 | 4 | distal | HMC3 |
| WDR81 | rs35048651 | rs11078596, rs11078597 | chr17:1618262 | 0.80 | MIR22HG | 1 | nearest | HMC3 |
| DOC2A | rs1140239 | rs4318227 | chr16:29984839 | 0.77 | HIRIP3, INO80E | 1 | distal | HMC3 |
| WDR12 | rs139643391 | rs72934512 | chr2:203926271 | 1.00 | ICA1L, NBEAL1 | 2 | nearest and distal | HMC3 |
| TPCN1 | rs6489896 | rs7297749, rs76097225 | chr12:113659752 | 1.00 | SLC8B1 | 1 | distal | HMC3 |
| TPCN1 | rs6489896 | rs73208737 | chr12:113635055 | 0.84 | SLC8B1 | 1 | distal | HMC3 |
| CASS4 | rs6069737 | rs927174 | chr20:55015166 | 0.89 | AURKA, CSTF1, RTFDC1, TCONS_00028450 | 2 | distal | HMC3 |
For each GWAS locus, proxy SNPs in open chromatin contacting an open gene promoter are reported, together with their sentinel SNPs, r2, target genes, and the number and type of interaction. Looping interactions and open chromatin maps were derived from promoter-focused Capture-C and ATAC-seq experiments in iMg and HMC3 cells.