Table 3.
Top-ranked ct-eQTLs in myeloid cell types.
| (A) Monocytes/macrophages | |||||||
|---|---|---|---|---|---|---|---|
| eGene | Lead eSNP | Positiona | MAF | Beta | Std error | P value | Number of significant eSNPs in gene/cell type |
| SLC12A1 | rs8037626 | 15:48606346 | 0.17 | −3.340 | 0.219 | 1.62E-52 | 126 |
| DLG2 | rs75798025 | 11:84018349 | 0.01 | 5.350 | 0.364 | 6.66E-49 | 597 |
| ABCA9 | rs4147976 | 17:66925923 | 0.44 | 0.872 | 0.068 | 1.97E-37 | 48 |
| PTPRG | rs116497321 | 3:62245373 | 0.01 | 2.650 | 0.221 | 3.96E-33 | 10 |
| CLNK | rs5028371 | 4:10452986 | 0.50 | 1.060 | 0.092 | 7.66E-31 | 272 |
| NFXL1 | rs10938499 | 4:47848377 | 0.33 | −1.270 | 0.112 | 8.38E-30 | 73 |
| FCRL5 | rs12760587 | 1:157526021 | 0.23 | 2.140 | 0.19 | 1.99E-29 | 93 |
| HLA-DRB5 | rs9269047 | 6:32438783 | 0.12 | −11.600 | 1.03 | 2.02E-29 | 1 |
| FMOD | NA | 1:203263699 | NA | 2.110 | 0.2 | 5.08E-26 | 42 |
| ABCA6 | rs144031521 | 17:67162715 | 0.01 | 8.620 | 0.833 | 4.27E-25 | 9 |
| INPP5F | rs181735165 | 10:121555618 | 0.02 | 7.150 | 0.701 | 1.99E-24 | 11 |
| RBMS3 | rs192885607 | 3:29612955 | 0.00 | 2.570 | 0.257 | 1.52E-23 | 34 |
| ARHGAP44 | NA | 17:12750576 | NA | 1.760 | 0.177 | 2.69E-23 | 54 |
| C4BPA | rs74148971 | 1:207275799 | 0.07 | −2.300 | 0.234 | 8.44E-23 | 24 |
| DCLK2 | rs114930380 | 4:150954757 | 0.03 | 1.630 | 0.169 | 5.16E-22 | 39 |
| PAM | NA | 5:102153433 | NA | −0.691 | 0.073 | 2.00E-21 | 47 |
| MYO1E | rs146483144 | 15:59422810 | 0.03 | 4.300 | 0.453 | 2.26E-21 | 17 |
| DSP | rs4960328 | 6:7495948 | 0.42 | 0.554 | 0.061 | 9.30E-20 | 6 |
| ROR1 | rs1557596882 | 1:64453767 | 0.01 | 3.570 | 0.393 | 1.05E-19 | 31 |
| CACNB2 | rs117299889 | 10:18404550 | 0.06 | 1.510 | 0.168 | 2.52E-19 | 61 |
| (B) Microglia | |||||||
|---|---|---|---|---|---|---|---|
| eGene | Lead eSNP | Positiona | MAF | Beta | Std error | P value | Number of significant eSNPs in gene/cell type |
| AC142381.1 | rs199931530 | 16:33047273 | 0.45 | −0.401 | 0.012 | 3.89E-233 | 43 |
| MLANA | rs201480524 | 9:68457329 | 0.50 | −0.176 | 0.007 | 4.82E-124 | 18 |
| AC015688.3 | rs62058902 | 17:25303954 | 0.50 | −0.213 | 0.009 | 1.94E-113 | 11 |
| HNRNPCL1 | rs75627772 | 1:13182567 | 0.00 | 0.186 | 0.008 | 4.31E-113 | 8 |
| AL050302.1 | rs3875276 | 21:14472722 | 0.50 | −0.890 | 0.040 | 2.62E-111 | 142 |
| ALLC | rs9808287 | 2:3624799 | 0.11 | 0.833 | 0.044 | 1.41E-79 | 12 |
| FAM21B | NA | 10:47917284 | NA | −2.210 | 0.118 | 2.88E-78 | 22 |
| WNT3 | rs9904865 | 17:44908263 | 0.37 | −1.570 | 0.084 | 3.90E-78 | 1 |
| RPL9 | rs1458255 | 4:39446549 | 0.28 | −2.370 | 0.137 | 4.76E-67 | 37 |
| HLA-DRB1 | rs72847627 | 6:32538512 | 0.32 | −2.130 | 0.125 | 4.15E-65 | 2305 |
| XRCC2 | rs80034602 | 7:152104360 | 0.50 | 2.120 | 0.128 | 1.30E-61 | 5 |
| WI2-3308P17.2 | rs4067785 | 1:120576209 | 0.50 | −0.184 | 0.011 | 1.33E-58 | 9 |
| DEFB121 | rs117541536 | 20:29422202 | 0.49 | −7.420 | 0.460 | 1.56E-58 | 1 |
| GINS1 | rs75374582 | 20:26109209 | 0.50 | −33.200 | 2.060 | 1.95E-58 | 5 |
| EXOSC10 | rs2580511 | 1:121113600 | 0.50 | −4.390 | 0.276 | 5.78E-57 | 5 |
| TRIM49B | rs202086299 | 11:48363026 | 0.50 | 0.205 | 0.013 | 2.16E-54 | 5 |
| TMPRSS9 | rs7248384 | 19:23936403 | 0.48 | −1.410 | 0.093 | 1.83E-52 | 1 |
| LDHC | NA | 11:18432033 | NA | 0.428 | 0.030 | 1.07E-47 | 73 |
| HLA-DOB | rs201194354 | 6:32796857 | NA | 1.190 | 0.084 | 4.39E-46 | 70 |
| DEFB119 | rs78099404 | 20:29617870 | 0.50 | −0.377 | 3.51E-15 | <1.0E-314 | 142 |
aMap position according to GRCh37 assembly.
MAF minor allele frequency, NA not available.