Table 2.
Regions containing SNPs for which the Omnibus GWAS test p< 5×10−5 and best-fitting models. SNP: single nucleotide polymorphism; CHR: chromosome; freq: minor allele frequency; G/I: genotyped or imputed SNP. Genotyped P: p-value of the genotyped SNP in the region. * first allele shown is minor allele.
| # SNPs |
CHR | Top SNP | Alleles* | Gene | Position | Freq BP1 |
Freq BP2 |
Freq SCZ |
Freq MDD |
Freq CTRL |
Bes Model | BIC Diff |
OMNIBUS P | G/I | Genotyped P |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 11 | rs6484218 | A/G | ADM | 61kb down | 0.13 | 0.07 | 0.13 | 0.13 | 0.14 | BP2 | 3.93E-08 | G | 3.93E-08 | |
| 3 | 22 | rs1001021 | A/G | MYO18B | intron 42 | 0.03 | 0.05 | 0.05 | 0.05 | 0.02 | SCZ_BPD_MDD | 2.39E-06 | G | 2.39E-06 | |
| 16 | 13 | rs7326068 | A/G | IFT88 | intron 16 | 0.18 | 0.23 | 0.16 | 0.23 | 0.19 | BP2_MDD | 2.92E-06 | G | 2.92E-06 | |
| 1 | 9 | rs3758354 | C/A | ANXA1 | 8kb up | 0.05 | 0.08 | 0.04 | 0.04 | 0.03 | BP2 | 3.31E-06 | G | 3.31E-06 | |
| 12 | 14 | rs4982029 | A/G | NPAS3 | intron 1 | 0.04 | 0.04 | 0.04 | 0.03 | 0.02 | SCZ_BPD_MDD | 3.96E-06 | I | 4.48E-06 | |
| 13 | 18 | rs11875674 | C/T | TXNL1 | 153kb up | 0.22 | 0.27 | 0.21 | 0.19 | 0.24 | BP2 | 3.97E-06 | I | 1.81E-05 | |
| 6 | 1 | rs4271171 | T/C | FAM20B | 8kb up | 0.53 | 0.58 | 0.49 | 0.54 | 0.5 | BPD_MDD | 4.12E-06 | I | 1.16E-05 | |
| 1 | 7 | rs12539410 | C/G | CHCHD3 | 403kb up | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | BP2_MDD | 4.74E-06 | I | -- | |
| 1 | 7 | rs4726220 | T/C | ACTR3B | 129kb down | 0.07 | 0.04 | 0.07 | 0.08 | 0.08 | BP2 | 1.16E-05 | G | 1.16E-05 | |
| 2 | 1 | rs17014011 | A/T | -- | intergenic | 0.13 | 0.15 | 0.16 | 0.15 | 0.11 | SCZ_BPD_MDD | 1.74E-05 | I | 2.36E-05 | |
| 4 | 2 | rs2372008 | G/A | CRIM1 | 782kb up | 0.44 | 0.38 | 0.45 | 0.38 | 0.41 | SCZ_BP1 | 1.78E-05 | G | 1.78E-05 | |
| 4 | 10 | rs7071307 | A/C | PPP2R2D | 360kb up | 0.43 | 0.49 | 0.46 | 0.42 | 0.42 | BP2 | 1.95E-05 | I | 1.98E-05 | |
| 1 | 5 | rs194487 | T/C | CTNND2 | intron 13 | 0.32 | 0.34 | 0.30 | 0.35 | 0.28 | BPD_MDD | 2.34E-05 | I | -- | |
| 2 | 2 | rs278865 | A/G | NR4A2 | 760kb up | 0.32 | 0.3 | 0.26 | 0.33 | 0.35 | SCZ | 2.46E-05 | I | -- | |
| 7 | 10 | rs10508451 | T/C | OPTN | 137kb up | 0.35 | 0.3 | 0.4 | 0.38 | 0.35 | BP2 | 2.87E-05 | G | 2.87E-05 | |
| 2 | 18 | rs12458992 | G/A | CCDC102B | 400kb up | 0.31 | 0.37 | 0.34 | 0.37 | 0.33 | BP2_MDD | 3.59E-05 | I | -- | |
| 1 | 15 | rs16949856 | T/C | -- | intergenic | 0.26 | 0.22 | 0.26 | 0.21 | 0.26 | BP2_MDD | 3.62E-05 | I | -- | |
| 1 | 15 | rs2117975 | A/G | EIF2AK4 | 91kb up | 0.15 | 0.11 | 0.10 | 0.15 | 0.15 | SCZ | 3.70E-05 | I | -- | |
| 10 | 20 | rs6079501 | G/T | SEL1L2 | 739kb down | 0.31 | 0.34 | 0.28 | 0.31 | 0.27 | BPD_MDD | 3.73E-05 | I | 3.82E-05 | |
| 4 | 12 | rs4140862 | A/C | TMEM16B | intron 5 | 0.3 | 0.33 | 0.33 | 0.36 | 0.36 | SCZ_BP1 | 4.03E-05 | I | 4.84E-05 | |
| 1 | 7 | rs917815 | G/A | SP8 | 270kb down | 0.4 | 0.32 | 0.35 | 0.4 | 0.4 | BP2 | 4.18E-05 | G | 4.18E-05 | |
| 1 | 3 | rs9819616 | G/A | RBMS3 | 294kb down | 0.35 | 0.34 | 0.39 | 0.31 | 0.36 | MDD | 4.46E-05 | I | -- | |
| 2 | 11 | rs11237798 | G/A | ODZ4 | 541kb down | 0.08 | 0.08 | 0.11 | 0.09 | 0.12 | BPD_MDD | 4.54E-05 | I | -- | |
| 1 | 21 | rs7280842 | T/C | SAMSN1 | 176kb down | 0.15 | 0.18 | 0.19 | 0.18 | 0.14 | SCZ_BPD_MDD | 4.56E-05 | G | 4.56E-05 | |
| 2 | 4 | rs7678609 | A/G | HAR39 | 26kb down | 0.36 | 0.32 | 0.33 | 0.34 | 0.29 | SCZ_BPD_MDD | 4.58E-05 | I | -- |