Summary statistics for other psychiatric conditions from previous GWAS studies were obtained as described in Supplementary Table 1. Association summary statistics for smoking and neuroticism in the UK Biobank were generated by GWAS (Supplementary Table 15 and 16, and Extended Data Fig. 3). We estimated the genetic correlation between definitions of MDD in the UK Biobank and each of these conditions using LDSC43, with an LD reference panel generated with European (EUR) individuals from 1000 Genomes68. To obtain regional rG, we partitioned the genome into 1,703 independent loci64 and estimated regional rG with rho-HESS46, using an LD reference panel generated with EUR individuals from 1000 Genomes68. We estimated s.e. for each regional rG and the total rG across the genome using a jackknife approach implemented in HESS36. To assess the percentage of genome contributing to total rG, we ranked all independent loci by their absolute value of regional rG, and asked how many loci would contribute 90% of the total rG.
