Table 1.
eQTLs and ct-eQTLs in established AD loci appearing in both blood and brain.
| (A) eQTLs and ct-eQTLS in established AD genes in both blood and brain. | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| eGene | Tissue | Cell type | Lead eSNP | Position | MAF | Beta | Std error | P value | Number of total significant eSNPs in gene/cell-type | AD GWAS peaks |
| CR1 | Blood | NA | rs7533408 | 1:207673631 | 0.25 | 0.059 | 0.006 | 3.60E-22 | 169 | NA |
| HLA-DRB5 | Blood | NA | rs9269008 | 6:32436217 | 0.17 | −2.580 | 0.057 | <1.0E-314 | 72 | NA |
| HLA-DRB1 | Blood | NA | rs9271058 | 6:32575406 | 0.14 | −2.950 | 0.028 | <1.0E-314 | 630 | Lead eSNP |
| ECHDC3 | Blood | NA | rs11257290 | 10:11780324 | 0.28 | 0.041 | 0.005 | 2.91E-19 | 115 | NA |
| WWOX | Blood | NA | rs7202722 | 16:78282458 | 0.40 | 0.023 | 0.003 | 2.60E-14 | 45 | NA |
| HLA-DRB5 | Blood | Interferon response(+)/antibacterial (−) | rs9269047 | 6:32438783 | 0.12 | −7.120 | 0.335 | 3.04E-100 | 9 [all (−)] | NA |
| HLA-DRB5 | Blood | Monocytes/macrophages | rs9269047 | 6:32438783 | 0.12 | −11.600 | 1.030 | 2.02E-29 | 1 | NA |
| HLA-DRB5 | Blood | NK cells/CD8 + T cells | rs9269047 | 6:32438783 | 0.12 | −7.660 | 0.994 | 1.30E-14 | 1 | NA |
| HLA-DRB1 | Blood | NK cells/CD8 + T cells | rs9270928 | 6:32572461 | 0.15 | −4.070 | 0.377 | 3.60E-27 | 287 | rs9271058 |
| HLA-DRB1 | Blood | Eosinophils | rs9270994 | 6:32574250 | 0.14 | −2.700 | 0.415 | 7.72E-11 | 42 | NA |
| HLA-DRB1 | Blood | Interferon response (+)/antibacterial (−) | rs9271147 | 6:32577385 | 0.14 | −5.510 | 0.250 | 1.19E-107 | 346 [260 (−)/86 (+)] | rs9271058 |
| HLA-DRB1 | Blood | Monocytes/macrophages | rs9271148 | 6:32577442 | 0.13 | −6.110 | 0.709 | 6.83E-18 | 222 | rs9271058 |
| CR1 | Brain | NA | rs12037841 | 1:207684192 | 0.17 | −0.096 | 0.007 | 9.25E-44 | 64 | rs6656401 |
| HLA-DRB5 | Brain | NA | rs3117116 | 6:32367017 | 0.12 | −2.780 | 0.070 | <1.0E-314 | 10537 | rs9271058, rs9271192 |
| HLA-DRB1 | Brain | NA | rs73399473 | 6:32538959 | 0.26 | −2.050 | 0.058 | 8.78E-272 | 10792 | rs9271058, rs9271192 |
| ECHDC3 | Brain | NA | rs866770710 | 10:11784320 | 0.0002 | −0.252 | 0.018 | 4.61E-44 | 45 | NA |
| WWOX | Brain | NA | rs12933282 | 16:78124987 | 0.45 | −0.133 | 0.017 | 1.13E-15 | 75 | NA |
| HLA-DRB5 | Brain | Microglia | rs67987819 | 6:32497655 | 0.14 | −1.900 | 0.137 | 9.82E-44 | 754 | NA |
| HLA-DRB5 | Brain | Endothelial cells | rs67987819 | 6:32497655 | 0.14 | −2.410 | 0.220 | 6.32E-28 | 343 | NA |
| HLA-DRB1 | Brain | Microglia | rs72847627 | 6:32538512 | 0.28 | −2.130 | 0.125 | 4.15E-65 | 2305 | rs9271058, rs9271192 |
| HLA-DRB1 | Brain | Neurons | rs115480576 | 6:32538570 | 0.26 | −2.210 | 0.153 | 2.72E-47 | 3263 | rs9271058, rs9271192 |
| HLA-DRB1 | Brain | Endothelial cells | rs9269492 | 6:32542924 | 0.30 | −2.250 | 0.243 | 2.06E-20 | 351 | rs9271192 |
| HLA-DRB5 | Brain | Neurons | rs9270035 | 6:32553446 | 0.14 | −2.520 | 0.137 | 1.46E-75 | 2540 | rs9271058, rs9271192 |
| ECHDC3 | Brain | Neurons | rs866770710 | 10:11784320 | 0.0002 | 0.328 | 0.045 | 3.13E-13 | 2 | NA |
| (B) eQTLs and ct-eQTLs involving AD GWAS association peak SNPs in both brain and blood. | ||||||||
|---|---|---|---|---|---|---|---|---|
| eGene | Tissue | Cell type | eSNP + GWAS SNP | Positiona | MAF | Beta | Std error | P value |
| HLA-DRB1 | Blood | NA | rs9271058 | 6:32575406 | 0.27 | −2.950 | 0.028 | <1.0E-314 |
| ARL17A | Blood | NA | rs2732703 | 17:44353222 | 0.21 | 0.147 | 0.023 | 5.95E-11 |
| ARL17A | Blood | NA | rs113986870 | 17:44355683 | 0.09 | 0.166 | 0.025 | 2.30E-11 |
| HLA-DRB1 | Blood | Interferon response (+)/antibacterial (−) | rs9271058 | 6:32575406 | 0.27 | −3.010 | 0.159 | 6.36E-80 |
| HLA-DRB1 | Blood | NK cells/CD8 + T cells | rs9271058 | 6:32575406 | 0.27 | −4.090 | 0.464 | 1.20E-18 |
| HLA-DRB1 | Blood | Monocytes/macrophages | rs9271058 | 6:32575406 | 0.27 | −3.540 | 0.497 | 1.06E-12 |
| HLA-DRB1 | Brain | NA | rs9271058 | 6:32575406 | 0.27 | −1.690 | 0.054 | 1.94E-213 |
| HLA-DRB5 | Brain | NA | rs9271058 | 6:32575406 | 0.27 | −1.770 | 0.081 | 2.28E-106 |
| LRRC37A2 | Brain | NA | rs2732703 | 17:44353222 | 0.21 | 1.370 | 0.053 | 4.13E-150 |
| LRRC37A2 | Brain | NA | rs113986870 | 17:44355683 | 0.09 | 1.260 | 0.068 | 1.98E-76 |
| ARL17A | Brain | NA | rs113986870 | 17:44355683 | 0.09 | −0.326 | 0.047 | 4.96E-12 |
| HLA-DRB1 | Brain | Microglia | rs9271058 | 6:32575406 | 0.27 | −1.400 | 0.111 | 1.80E-36 |
| HLA-DRB1 | Brain | Neurons | rs9271058 | 6:32575406 | 0.27 | −1.650 | 0.135 | 2.37E-34 |
| HLA-DRB5 | Brain | Neurons | rs9271058 | 6:32575406 | 0.27 | −1.550 | 0.201 | 1.24E-14 |
| LRRC37A2 | Brain | Neurons | rs2732703 | 17:44353222 | 0.21 | 1.520 | 0.140 | 1.84E-27 |
| LRRC37A2 | Brain | Microglia | rs2732703 | 17:44353222 | 0.21 | 1.480 | 0.147 | 7.65E-24 |
| LRRC37A2 | Brain | Endothelial cells | rs2732703 | 17:44353222 | 0.21 | 1.750 | 0.233 | 5.88E-14 |
| LRRC37A2 | Brain | Microglia | rs113986870 | 17:44355683 | 0.09 | 1.530 | 0.195 | 4.29E-15 |
| LRRC37A2 | Brain | Neurons | rs113986870 | 17:44355683 | 0.09 | 1.400 | 0.184 | 2.77E-14 |
aPosition according to GRCh37 assembly.
MAF = minor allele frequency of variant in 1000 Genomes Combined European Population; cell-type-specific result rows are in bold.