Table 2.
Independent loci identified by cortical PAM GWAS
| PAM region | Ch | Lead SNP | SNP position | A1 | A2 | Freq (A1) | Beta (A1) | P-value | Genes mapped to locus (combined positional and/or eQTL mapping) |
|---|---|---|---|---|---|---|---|---|---|
| MF | 1 | rs2997325 | 83641424 | A | T | 0.629 | −0.0389 | 1.88E−08 | RP11-170N11.1 |
| 1 | rs157864 | 165383761 | T | C | 0.1415 | 0.0443 | 8.60E−06 | RXRG | |
| 1 | rs651691 | 193958320 | T | C | 0.5531 | 0.0317 | 6.45E−06 | ||
| 2 | rs12623587 | 232160554 | A | C | 0.29 | −0.0321 | 6.00E−06 | C2orf72, PSMD1, HTR2B, ARMC9 | |
| 3 | rs78461316 | 104858434 | T | C | 0.0587 | 0.0749 | 2.54E−07 | ||
| 7 | rs141219652 | 70367062 | C | T | 0.0226 | 0.1083 | 8.72E−06 | ||
| 10 | rs61860520 | 134826645 | T | C | 0.0543 | −0.0719 | 4.02E−06 | TTC40, LINC01166 | |
| 11 | rs138662357 | 92058950 | C | A | 0.0555 | 0.074 | 3.49E−07 | NDUFB11P1, FAT3, PGAM1P9 | |
| 13 | rs9514523 | 106927120 | T | C | 0.1871 | −0.0386 | 9.20E−06 | ||
| 13 | rs9521336 | 110023731 | C | T | 0.2146 | 0.0378 | 1.96E−06 | MYO16-AS1, LINC00399 | |
| 14 | rs2105997 | 107209226 | T | A | 0.2276 | 0.0388 | 8.46E−06 | IGHV4-39, HOMER2P1, IGHV4-61, IGHV3-64, IGHV3-66, IGHV1-69, IGHV3-72, IGHV3-73, IGHV3-74 | |
| 15 | rs144705301 | 67855035 | C | T | 0.0263 | 0.11 | 1.74E−07 | AAGAB, RPS24P16, MAP2K5, SKOR1 | |
| IT | 1 | rs56267558 | 21005316 | T | G | 0.1287 | 0.0431 | 6.40E−06 | MUL1, CDA, PINK1, PINK1-AS, DDOST, KIF17 |
| 1 | rs113285275 | 70896319 | A | G | 0.2344 | −0.0328 | 3.10E−06 | HHLA3, CTH | |
| 1 | rs183093970 | 88454261 | G | A | 0.0147 | 0.1535 | 5.47E−10 | ||
| 1 | rs147836155 | 113501607 | T | C | 0.0129 | 0.1346 | 2.46E−06 | SLC16A1, SLC16A1-AS1 | |
| 2 | rs148259393 | 28713654 | G | C | 0.0204 | 0.1038 | 3.30E−06 | PLB1 | |
| 2 | rs141418970 | 40576095 | T | G | 0.0102 | 0.1593 | 4.82E−07 | SLC8A1 | |
| 2 | rs17018138 | 80154236 | G | C | 0.05 | 0.0588 | 7.53E−06 | CTNNA2 | |
| 2 | rs79341575 | 129133292 | C | G | 0.0551 | 0.063 | 2.75E−06 | GPR17 | |
| 2 | rs60200364 | 160708050 | A | G | 0.0623 | 0.0555 | 2.14E−06 | BAZ2B, LY75, LY75-CD302, PLA2R1, ITGB6 | |
| 2 | rs2348117 | 201598521 | T | G | 0.8893 | −0.0414 | 9.76E−06 | AOX3P, AOX2P, AC007163.3, PPIL3, RNU6-312P | |
| 3 | rs9289581 | 139405842 | T | G | 0.37 | 0.0271 | 8.32E−06 | NMNAT3 | |
| 4 | rs7656795 | 22398514 | T | C | 0.8175 | −0.037 | 1.22E−06 | GPR125 | |
| 4 | rs114105899 | 23027094 | G | A | 0.0158 | 0.1197 | 8.10E−07 | RP11-412P11.1 | |
| 4 | rs10011717 | 86136864 | A | G | 0.3774 | −0.0282 | 6.09E−06 | ||
| 4 | rs77601419 | 148249054 | T | C | 0.015 | 0.1168 | 2.22E−06 | ||
| 7 | rs77033896 | 115513816 | A | G | 0.0169 | 0.1262 | 6.84E−07 | TFEC, CAV1 | |
| 8 | rs17494322 | 20673550 | G | A | 0.075 | 0.0535 | 4.18E−06 | ||
| 11 | rs139629925 | 76144667 | G | A | 0.0121 | 0.1347 | 5.91E−06 | RP11-111M22.2, C11orf30, LRRC32 | |
| 11 | rs2084308 | 111051351 | T | A | 0.028 | 0.0967 | 4.29E−07 | ||
| 13 | rs7328235 | 41998022 | T | C | 0.9439 | −0.0607 | 6.72E−06 | MTRF1, OR7E36P | |
| 13 | rs9567982 | 48605441 | G | A | 0.1375 | 0.0394 | 3.08E−06 | LINC00444, LINC00562, SUCLA2, SUCLA2-AS1, NUDT15, MED4, MED4-AS1, POLR2KP2 | |
| 13 | rs117372720 | 61819169 | T | C | 0.0149 | 0.1092 | 8.97E−06 | ||
| 13 | rs149383020 | 112585032 | A | G | 0.0341 | 0.0787 | 5.09E−07 | ||
| 14 | rs144434563 | 91361842 | G | A | 0.0135 | 0.1265 | 6.79E−06 | RPS6KA5 | |
| 14 | rs137899216 | 91830706 | T | C | 0.0277 | 0.0911 | 3.06E−06 | GPR68, CCDC88C, SMEK1 | |
| 17 | rs112645358 | 66248531 | T | C | 0.0384 | 0.069 | 9.94E−06 | KPNA2, LRRC37A16P, AMZ2, ARSG | |
| 18 | rs148222222 | 65675614 | T | C | 0.0169 | 0.1133 | 1.47E−06 | RP11-638L3.1 | |
| 20 | rs71336998 | 5467150 | G | A | 0.018 | 0.1266 | 1.17E−07 | LINC00654 |
Ch chromosome, A1 allele 1 (effect allele), A2 allele 2, eQTL expression quantitative trait loci, Freq allele frequency, IT inferior temporal cortex, MF midfrontal cortex