Table 2.
81 genes of gene-based association results in the discovery sample for hippocampal volume using common variants (MAF ≥ 0.05) where empirical p-values were calculated using 20,000 permutations in PLINK
| Gene | Number of SNPs in gene |
Number of significant SNPs (p<0.05, r2<0.5) |
Empirical gene-based p-value |
List of significant SNP |
|---|---|---|---|---|
| ADORA2A | 55 | 1 | 5×10−5 | rs9608282 |
| APOE | 85 | 5 | 5×10−5 | rs429358|rs7259620|rs34095326|rs4803770|rs157580 |
| TLR4 | 58 | 2 | 0.01499 | rs11789302|rs10759930 |
| BCHE | 201 | 4 | 0.02797 | rs2686409|rs1355538|rs12107166|rs6807910 |
| CXCL10 | 42 | 1 | 0.04795 | rs4256246 |
| S100B | 220 | 1 | 0.05994 | rs118078026 |
| CXCL12 | 306 | 4 | 0.06194 | rs11238990|rs11238991|rs1144472|rs17659345 |
| TET1 | 387 | 3 | 0.06593 | rs113716271|rs12776586|rs12221107 |
| BCL2 | 368 | 5 | 0.07493 | rs9957149|rs28564323|rs7236090|rs6567334|rs11872403 |
| PTGS2 | 52 | 2 | 0.08492 | rs7547677|rs2206593 |
| ACHE | 51 | 2 | 0.08791 | rs13245899|rs73714210 |
| SORL1 | 233 | 2 | 0.09091 | rs9665907|rs643010 |
| SLC6A4 | 63 | 1 | 0.09191 | rs16965628 |
| GRIN2B | 1054 | 5 | 0.0999 | rs34870448|rs11612709|rs12582848|rs11611667|rs2300256 |
| NGFR | 86 | 5 | 0.0999 | rs584589|rs11466150|rs2072444|rs535717|rs2537710 |
| MEF2C | 232 | 1 | 0.1019 | rs1065861 |
| CXCL1 | 39 | 1 | 0.1039 | rs2968710 |
| NR3C1 | 238 | 5 | 0.1209 | rs4912912|rs17209237|rs10050756|rs7719514|rs12653301 |
| DKK1 | 40 | 2 | 0.1249 | rs11001581|rs7100461 |
| GRN | 37 | 1 | 0.1319 | rs114641762 |
| CHAT | 189 | 5 | 0.1379 | rs885834|rs11101179|rs1720367|rs4615945|rs74981858 |
| CHRNB2 | 39 | 5 | 0.1499 | rs9616|rs9427094|rs12072348|rs67860750|rs4845653 |
| Syn3 | 1388 | 5 | 0.1718 | rs2157188|rs9609643|rs2710348|rs180958069|rs5749521 |
| CCL2 | 43 | 1 | 0.1758 | rs111843487 |
| IGF1 | 89 | 4 | 0.1888 | rs1549593|rs10860862|rs12821878|rs80280982 |
| VEGFA | 59 | 3 | 0.1908 | rs9381248|rs3025006|rs699946 |
| NGF | 135 | 2 | 0.1978 | rs6537860|rs4320778 |
| MIF | 77 | 1 | 0.2008 | rs738807 |
| IL6 | 77 | 2 | 0.2338 | rs2069840|rs62449498 |
| CASP3 | 94 | 2 | 0.2378 | rs4647634|rs2696059 |
| MMP9 | 57 | 2 | 0.2537 | rs73112805|rs3918253 |
| PRNP | 94 | 2 | 0.2747 | rs6052766|rs67017873 |
| SNCA | 444 | 1 | 0.2927 | rs187644542 |
| CDK5 | 53 | 2 | 0.3147 | rs4148853|rs34403003 |
| IL1B | 42 | 1 | 0.3147 | rs3917381 |
| ADAM10 | 232 | 1 | 0.3197 | rs544282 |
| NOS3 | 71 | 1 | 0.3197 | rs12666075 |
| NRG1 | 2784 | 5 | 0.3227 | rs147179882|rs2466068|rs7829383|rs2347071|rs11998153 |
| APBB1 | 119 | 1 | 0.3487 | rs11040880 |
| LRRK2 | 360 | 3 | 0.3526 | rs189800607|rs10878411|rs11564173 |
| OLIG2 | 123 | 2 | 0.3626 | rs17632819|rs76708155 |
| NOS1 | 559 | 5 | 0.3826 | rs67313272|rs4767542|rs816284|rs12228022|rs10850829 |
| HIF1A | 82 | 1 | 0.4186 | rs12891737 |
| FGF1 | 221 | 5 | 0.4326 | rs1808258|rs2070715|rs249925|rs10041541|rs13179022 |
| TGFB1 | 131 | 1 | 0.5135 | rs4803459 |
| IGF1R | 520 | 5 | 0.5325 | rs11631965|rs4966039|rs3743254|rs7166348|rs2272037 |
| FAS | 175 | 1 | 0.5774 | rs12767306 |
| APP | 554 | 5 | 0.6214 | rs2829960|rs6516705|rs13046930|rs6516715|rs117104544 |
| NTRK2 | 605 | 4 | 0.6264 | rs17087710|rs28580203|rs1047896|rs1006446 |
| DYRK1A | 380 | 1 | 0.6593 | rs28550863 |
| ESR2 | 412 | 4 | 0.6983 | rs1152576|rs4986938|rs10146107|rs12587140 |
| RELN | 1552 | 5 | 0.7932 | rs2299373|rs3819491|rs39377|rs1476446|rs694894 |
| ESR1 | 810 | 1 | 0.7972 | rs55650062 |
| ABCA2 | 61 | 0 | 1 | NA |
| ADRA2A | 27 | 0 | 1 | NA |
| BDNF | 122 | 0 | 1 | NA |
| CAV1 | 129 | 0 | 1 | NA |
| CDK5R1 | 24 | 0 | 1 | NA |
| CHRNA7 | 2 | 0 | 1 | NA |
| CNTF | 29 | 0 | 1 | NA |
| FOS | 48 | 0 | 1 | NA |
| GSK3B | 329 | 0 | 1 | NA |
| HTR2A | 203 | 0 | 1 | NA |
| NEUROD1 | 54 | 0 | 1 | NA |
| NPY | 131 | 0 | 1 | NA |
| PLCG1 | 60 | 0 | 1 | NA |
| PSEN1 | 154 | 0 | 1 | NA |
| SIRT1 | 98 | 0 | 1 | NA |
| THRA | 82 | 0 | 1 | NA |
| TNF | 40 | 0 | 1 | NA |
| TNFR1A | 4 | 0 | 1 | NA |
| TNFR1B | 54 | 0 | 1 | NA |
| DLD | 24 | 0 | 1 | NA |
| GLP1R | 98 | 0 | 1 | NA |
| IFNG | 19 | 0 | 1 | NA |
| Plau | 30 | 0 | 1 | NA |
| PSEN2 | 19 | 0 | 1 | NA |
| SOD2 | 5 | 0 | 1 | NA |
| tp53 | 5 | 0 | 1 | NA |
| CST3 | 92 | 0 | 1 | NA |
| CHRM1 | 47 | 0 | 1 | NA |