Table 2.
Genes reaching statistical significance (FDR ≤ 0.05) for association with MDD conditional on association with LOAD.
| SNP | Chr | Positiona | Nearest gene | Minor allele | MAF | Conditional FDR Q(MDD|LOAD) | LOAD Beta | LOAD Beta SE | LOAD P-value | MDD OR | MDD OR SE | MDD P-value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs35591392 | 14 | 75,157,713 | AREL1 | T | 0.53 | 2.82E–02 | −0.047 | 0.014 | 8.83E−04 | 1.031 | 0.008 | 9.03E−05 |
| rs78563874 | 11 | 85,609,073 | CCDC83 | T | 0.24 | 2.76E–02 | 0.064 | 0.017 | 1.46E−04 | 0.964 | 0.009 | 9.09E−05 |
| rs57105978 | 5 | 26,843,262 | CDH9 | T | 0.03 | 2.02E–02 | 0.109 | 0.036 | 2.61E−03 | 0.930 | 0.019 | 1.20E−04 |
| rs2071408 | 14 | 103,987,078 | CKB | A | 0.37 | 1.44E–02 | 0.049 | 0.015 | 1.12E−03 | 0.961 | 0.009 | 3.09E−06 |
| rs7508819 | 20 | 49,205,320 | FAM65C | T | 0.58 | 1.94E–02 | 0.047 | 0.015 | 1.34E−03 | 1.031 | 0.008 | 1.79E−04 |
| rs202675 | 11 | 49,228,613 | FOLH1 | C | 0.28 | 1.79E–02 | −0.054 | 0.016 | 7.43E−04 | 0.968 | 0.009 | 1.50E−04 |
| rs74018295 | 15 | 57,870,174 | GCOM1 | T | 0.09 | 1.90E–02 | −0.077 | 0.026 | 3.13E−03 | 0.946 | 0.015 | 1.74E−04 |
| rs111666866 | 6 | 32,491,925 | HLA-DRB5 | T | 0.73 | 4.85E–02 | 0.060 | 0.018 | 8.22E−04 | 0.966 | 0.010 | 6.14E−04 |
| rs4900582 | 14 | 104,058,014 | KLC1 | A | 0.64 | 2.48E–02 | 0.052 | 0.016 | 8.84E−04 | 0.969 | 0.009 | 2.68E−04 |
| rs8106047 | 19 | 18,505,741 | LRRC25 | A | 0.16 | 4.31E–02 | 0.068 | 0.023 | 2.82E−03 | 0.941 | 0.014 | 1.30E−05 |
| rs2894221 | 6 | 31,461,771 | MICB | A | 0.36 | 3.79E–02 | −0.047 | 0.015 | 1.75E−03 | 0.968 | 0.008 | 7.42E−05 |
| rs6664244 | 1 | 40,374,386 | MYCL | T | 0.36 | 2.47E–02 | −0.057 | 0.015 | 1.32E−04 | 0.971 | 0.008 | 2.67E−04 |
| rs7103992 | 11 | 48,510,777 | OR4A47 | A | 0.65 | 2.84E–02 | −0.045 | 0.015 | 2.26E−03 | 0.969 | 0.008 | 8.98E−05 |
| rs10838830 | 11 | 48,233,932 | OR4B1 | A | 0.35 | 2.42E–02 | −0.044 | 0.015 | 3.06E−03 | 0.971 | 0.008 | 2.54E−04 |
| rs4312096 | 11 | 48,411,653 | OR4C5 | C | 0.65 | 1.93E–02 | −0.045 | 0.015 | 2.66E−03 | 0.969 | 0.008 | 1.79E−04 |
| rs3009872 | 1 | 66,411,400 | PDE4B | T | 0.43 | 3.87E–02 | 0.044 | 0.014 | 2.05E−03 | 1.028 | 0.008 | 4.68E−04 |
| rs1265099 | 6 | 31,105,413 | PSORS1C1 | A | 0.42 | 3.75E–02 | 0.048 | 0.015 | 1.07E−03 | 1.036 | 0.008 | 8.88E−06 |
| rs6063534 | 20 | 49,189,168 | PTPN1 | T | 0.51 | 1.80E–02 | 0.043 | 0.014 | 2.33E−03 | 1.031 | 0.008 | 1.36E−04 |
| rs12790666 | 11 | 47,983,477 | PTPRJ | A | 0.52 | 1.79E–02 | −0.045 | 0.014 | 1.71E−03 | 0.970 | 0.008 | 1.42E−04 |
| rs12668707 | 7 | 4,414,425 | SDK1 | C | 0.21 | 4.36E–02 | −0.051 | 0.017 | 2.98E−03 | 1.034 | 0.010 | 5.38E−04 |
| rs111653412 | 6 | 3,370,053 | SLC22A23 | T | 0.02 | 2.38E–02 | 0.191 | 0.065 | 3.15E−03 | 0.863 | 0.040 | 2.47E−04 |
| rs10157030 | 1 | 246,184,138 | SMYD3 | T | 0.28 | 2.23E–02 | 0.056 | 0.016 | 5.73E−04 | 1.034 | 0.009 | 2.24E−04 |
| rs6122859 | 20 | 48,610,609 | SNAI1 | A | 0.63 | 3.99E–02 | −0.047 | 0.015 | 2.12E−03 | 0.971 | 0.008 | 4.86E−04 |
| rs7785189 | 7 | 12,257,527 | TMEM106B | T | 0.41 | 3.31E–02 | −0.045 | 0.014 | 1.53E−03 | 1.032 | 0.008 | 7.77E−05 |
| rs4268511 | 11 | 49,046,510 | TRIM49B | A | 0.64 | 1.81E–02 | 0.056 | 0.015 | 2.08E–04 | 1.032 | 0.008 | 1.32E−04 |
| rs7949585 | 11 | 49,077,746 | TRIM64C | T | 0.60 | 2.00E–02 | −0.051 | 0.015 | 6.11E–04 | 0.970 | 0.008 | 1.90E−04 |
| rs911552 | 14 | 103,999,508 | TRMT61A | A | 0.37 | 8.94E–03 | −0.051 | 0.015 | 5.98E–04 | 1.042 | 0.009 | 1.73E–06 |
SNP single-nucleotide polymorphism, MAF minor allele frequency, LOAD late-onset Alzheimer’s disease, MDD major depressive disorder, FDR false discovery rate.
aBuild 37, assembly hg19.