Table 2.
Summary statistics for 17 SNPs reaching genome-wide significance (pval < 5×10−8) in the joint analysis (23andMe Discovery, PGC, and 23andMe replication dataset). Corresponding pvalues, effect, and standard error shown for each phase of analysis: 23andMe MDD (Discovery dataset), PGC MDD, meta-analysis (23andMe Discovery + PGC), 23andMe Replication (23andme Replication cohort), and joint analysis. Effect and standard error are unadjusted. Pvalues are adjusted for 23andMe Discovery, PGC, and meta-analysis
| rs ID | Gene Context | 23andMe | PGC | Meta | Replication* | Joint* | sign-match |
|---|---|---|---|---|---|---|---|
| rs10514299 | TMEM161B–[]—MEF2C | 4.35E-12 | 5.73E-01 | 8.50E-11 | 1.15E-04 | 9.99E-16 | Y |
| rs1518395 | []–VRK2 | 1.45E-07 | 5.83E-01 | 2.01E-07 | 1.50E-05 | 4.32E-12 | Y |
| rs2179744 | [L3MBTL2] | 4.34E-08 | 7.74E-01 | 9.24E-08 | 7.26E-04 | 6.03E-11 | Y |
| rs11209948 | NEGR1–[] | 4.41E-08 | 8.57E-02 | 1.01E-08 | 9.39E-04 | 8.38E-11 | Y |
| rs454214 | TMEM161B—[]–MEF2C | 6.28E-08 | 1.62E-01 | 2.42E-08 | 6.39E-03 | 1.09E-09 | Y |
| rs301806 | [RERE] | 3.72E-06 | 8.68E-01 | 7.28E-06 | 2.52E-04 | 1.90E-09 | Y |
| rs1475120 | HACE1–[]–LIN28B | 2.32E-06 | 2.29E-01 | 1.14E-06 | 9.27E-04 | 4.17E-09 | Y |
| rs10786831 | [SORCS3] | 1.75E-06 | 2.98E-01 | 1.09E-06 | 2.33E-03 | 8.11E-09 | Y |
| rs12552 | [OLFM4] | 1.23E-12 | 1.57E-01 | 5.74E-13 | 8.70E-01 | 8.16E-09 | N |
| rs6476606 | [PAX5] | 2.59E-05 | 1.52E-01 | 9.30E-06 | 1.94E-04 | 1.20E-08 | Y |
| rs8025231 | MEIS2—[]—TMCO5A | 2.04E-08 | 8.49E-02 | 4.66E-09 | 7.50E-02 | 1.23E-08 | Y |
| rs12065553 | [] | 8.53E-07 | 8.67E-01 | 2.88E-06 | 6.79E-03 | 1.32E-08 | Y |
| rs1656369 | RSRC1–[]-MLF1 | 8.19E-08 | 3.22E-01 | 6.05E-08 | 3.56E-02 | 1.34E-08 | Y |
| rs4543289 | [] | 1.19E-06 | 1.15E-02 | 8.23E-08 | 5.26E-03 | 1.36E-08 | Y |
| rs2125716 | []—SLC6A15 | 4.33E-07 | 8.78E-01 | 9.58E-07 | 2.24E-02 | 3.05E-08 | Y |
| rs2422321 | NEGR1—[] | 5.12E-06 | 6.91E-03 | 3.28E-07 | 3.13E-03 | 3.18E-08 | Y |
| rs7044150 | KIAA0020—[]—RFX3 | 3.97E-07 | 9.64E-01 | 1.24E-06 | 3.05E-02 | 4.31E-08 | Y |
meta-analysis and replication not adjusted for inflation in joint analysis
Adjustments were done using LD score regression calculated intercepts. Sign-match is shown for matching of direction of effect between the meta-analysis and 23andMe replication datasets. All alleles are on the (+) or forward genomic strand. All effects are reported for the 2nd allele when listed in alphabetical order. Text representation of SNP location in relation to other genes in the region is shown. The SNP location is denoted by []. If the SNP occurs between genes then the distance from those genes are denoted by dashes (−), with ‘’ = <1kb, ‘−‘ = <10kb, ‘−−‘ = <100kb, ‘−−−‘ = <1000kb. HG19 release of UCSC was used for mapping. EAF= effect allele frequency for controls. Results for GWAS results are peak-pruned by distance (300 kb) and LD (r2 > 0.1)