2. Regional association plots for this SNP in other depression subtypes are shown in Supplementary Figure 4, demonstrating that this locus does not replicate in any other depression subtype (minimum P = 8.05 × 10−4 in MDD, β(SE) = 0.10(0.05)). Full details of all independent loci used in downstream analyses (P ≤ 1 × 10−5) are shown in Supplementary Tables 4-11. The QQ plots (Supplementary Figure 3) demonstrate λGC ranged from 1.02–1.06, comparable to the value (1.056) observed in the PGC mega-analysis of MDD2. Univariate LDSR analyses estimated that meta-analyzed MDD subtypes had mean chi-squared statistic (μχ2) values ranging from 1.018 (mMDD) to 1.062 (MDD) with a Ratio, defined as (Intercept-1)/(μχ2-1), ≤ 0.35 across subtypes, indicating that any inflation in μχ2 can be attributed to polygenicity rather than residual population stratification36.Table 1Summary statistics for SNPs with association P-value ≤ 1 × 10−6 for depression (MDD), recurrent depression (rMDD), depression in females only (fMDD) and depression in males only (mMDD), sorted within phenotype by genomic positions according to UCSC hg19/NCBI Build 37 Trait SNP CHR POS A1/A2 Freq β(se) P Direction Genes MDDrs563905034187552576T/C0.110.13 (0.03)9.08E–07++ FAT1 rs2964802510820843T/C0.280.09 (0.02)6.73E–07++-rs110333031135871266A/G0.370.09 (0.02)2.37E–07++-rMDDrs22914793178174944A/C0.4−0.10 (0.02)9.65E–07---rs10959631911220986T/C0.2−0.12 (0.02)8.34E-07---rs110333031135871266A/G0.370.11 (0.02)6.02E–07++-rs443817213111448658A/T0.250.11 (0.02)8.72E–07++-fMDDrs9648182713794849A/T0.12−0.17 (0.03)9.14E–08-- - rs17176546781880914A/G0.040.26 (0.05)7.93E–07++ CACNA2D1 mMDDrs1157361671155266609C/G0.02−0.46 (0.09)1.54E–07-- PKLR rs4478037333160407A/G0.080.29
