Table 5 Significantly AD-associated probes/genes from transcriptome-wide analyses
From: Genome-wide analysis of genetic predisposition to Alzheimer’s disease and related sex disparities
Probe ID | Gene | Top eQTL | Chromosomal region | Position | A1 | A1 Freq | P GWAS | P eQTL | b SMR | SESMR | P SMR | P HEIDI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Plan 1—males and females | ||||||||||||
ILMN_1754501 | C2orf74 | rs720201 | 2p15 | 61,149,328 | C | 0.413 | 6.94E–04 | 1.34E–164 | 0.189 | 0.047 | 5.54E–05 | 6.64E–01 |
ILMN_2206098 | ATG10 | rs11741569 | 5q14.1 | 82,030,091 | G | 0.090 | 9.96E–04 | 9.69E–27 | −0.391 | 0.097 | 5.66E–05 | 8.32E–02 |
ILMN_2359800 | MS4A6A | rs7108663 | 11q12.2 | 60,260,669 | C | 0.412 | 2.17E–04 | 1.41E–48 | 0.380 | 0.088 | 1.59E–05 | 8.57E–01 |
ILMN_2343047 | ABCB9 | rs641760 | 12q24.31 | 123,034,319 | T | 0.214 | 2.75E–04 | 9.79E–17 | −0.650 | 0.162 | 6.03E–05 | 1.14E–01 |
Plan 2—only males | ||||||||||||
ILMN_1700307 | ZNF815 | rs117856560 | 7p22.1 | 5,852,503 | C | 0.048 | 1.50E–02 | 8.23E–49 | 0.389 | 0.092 | 2.22E–05 | 8.80E–02 |
ILMN_1731043 | TRA2A | rs1046135 | 7p15.3 | 23,530,965 | T | 0.135 | 1.89E–03 | 4.32E–115 | −0.294 | 0.067 | 1.07E–05 | 2.51E–01 |
ILMN_1671603 | MED30 | rs10111328 | 8q24.11 | 117,525,450 | T | 0.426 | 3.79E–04 | 1.67E–20 | 1.011 | 0.232 | 1.30E–05 | 8.22E–02 |
ILMN_1742789 | LPXN | rs7928565 | 11q12.1 | 58,587,146 | C | 0.012 | 2.47E–02 | 7.17E–86 | −0.287 | 0.056 | 2.68E–07 | 6.20E–01 |
ILMN_1913678 | IRAK3 | rs1436849 | 12q14.3 | 66,181,338 | T | 0.416 | 1.25E–03 | 6.14E–35 | −0.656 | 0.160 | 4.11E–05 | 6.60E–02 |
ILMN_1737561 | N4BP2L2 | rs718444 | 13q13.1 | 32,572,915 | T | 0.375 | 1.16E–03 | 1.80E–53 | −0.489 | 0.119 | 3.96E–05 | 2.90E–01 |
ILMN_1724734 | UQCC | rs2425062 | 20q11.22 | 35,335,763 | G | 0.383 | 2.01E–04 | 4.58E–13 | −1.356 | 0.321 | 2.42E–05 | 7.78E–01 |
ILMN_2296950 | APOBEC3F | rs11089928 | 22q13.1 | 39,133,424 | A | 0.068 | 2.42E–03 | 7.21E–20 | −0.724 | 0.168 | 1.60E–05 | 8.31E–02 |
ILMN_1806607 | SFN a | rs3817604 | 1p36.11/4p16.3 | 1,297,549 | T | 0.120 | 4.10E–04 | 5.77E–10 | 1.179 | 0.292 | 5.49E–05 | 3.92E–01 |
Plan 3—only females | ||||||||||||
ILMN_1806710 | ESPN | rs12074379 | 1p36.31 | 6,434,683 | T | 0.040 | 7.26E–03 | 8.51E–40 | 0.421 | 0.101 | 3.38E–05 | 2.84E–01 |
ILMN_1696003 | GNAI3 | rs2301229 | 1p13.3 | 109,594,056 | T | 0.175 | 4.92E–04 | 1.45E–211 | −0.209 | 0.045 | 4.00E–06 | 1.21E–01 |
ILMN_1741881 | C9orf72 | rs2282240 | 9p21.2 | 27,572,636 | T | 0.264 | 2.49E–04 | 1.18E–90 | −0.327 | 0.070 | 3.27E–06 | 5.39E–02 |
ILMN_1803925 | MTMR3 | rs41174 | 22q12.2 | 30,030,080 | T | 0.325 | 8.34E–04 | 3.03E–76 | 0.321 | 0.078 | 4.21E–05 | 4.12E–01 |