We used stratified LDSC regression to estimate the SNP-based heritability of depression, using the sample prevalence as the population prevalence (0.302), and then examined the heritability of partitioned functional categories 71. This method assigns variants into 24 functional categories and then evaluates the contribution of each category to the overall heritability of a trait. A category is enriched for heritability if the variants with high LD to that category have elevated χ2 statistics. The 24 categories are described in full in the Finucane et al. paper 71. Briefly, they include genetic annotations from ReqSeq gene models 72, transcription factor binding sites from ENCODE 72, 73, Roadmap epigenomics annotations 74, super-enhancers 75, evolutionarily conserved regions 76 and FANTOM5 enhancers 77. Heritability enrichment is defined as the proportion of heritability assigned to a functional category divided by the proportion of variants in that category. Cell-type specific annotations were also analysed for variants in four histone marks: H3K4me1, H3K4me3, H3K9ac and H3K27ac and these were grouped into 9 cell type groups: central nervous system (CNS), cardiovascular, connective tissue or bone, gastrointestinal, immune or
