One genomic region on chromosome 3p22.3 achieved genome-wide significance in the males only case/control (mMDD) analysis (index SNP rs4478037, β(SE) = 0.29(0.05), P = 2.29 × 10−8). None of the SNPs achieving genome-wide significance (nSNPs = 6) associated with any phenotype in currently published GWAS available via the NHGRI-EBI catalog. One variant (rs7613051) within the local genomic region (defined 3:33000000–33200000) has previously shown an association with Atopic dermatitis60, however this SNP is not in LD with the genome-wide significant SNPs (r2 < 0.1). Meta-analysis of MDD, rMDD, and fMDD did not yield any genome-wide significant findings. Manhattan plots are shown for each trait in Fig. 1, and summary statistics for independent loci with a meta-analysis association P ≤ 1 × 10−6 are shown in Table 1. A regional association plot for genome-wide significant index SNP, rs4478037, is shown in Fig. 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)).
