Additionally we expanded the cell-type specific heritability analysis by including an annotation based on information about H3K4Me1 imputed gapped peaks excluding the broad MHC-region (chr6:25–35MB), generated by the Roadmap Epigenomics Mapping Consortium121,122 (Supplementary Information). The analyses were restricted to the European GWAS meta-analysis results to ensure matching of population LD structure. Results for each functional category were evaluated based on marginal enrichment, defined as the proportion of SNP heritability explained by SNPs in the annotation divided by the proportion of genome-wide SNPs in the annotation40. For each cell-type group and each H3K4Me1 cell-type annotations, the contribution to SNP heritability was tested conditional on the baseline model containing the 53 functional categories.
