We partitioned SNP heritability using stratified LD Score regression42 in three ways: 1) by functional annotation category, 2) by minor allele frequency (MAF) in six percentile bins, and 3) by chromosome. Annotations for 28 binary categories of putative functional genomic characteristics (e.g. coding or regulatory regions) were obtained from the LD score website (see URLs). With this method, enrichment/depletion of heritability in each category is calculated as the proportion of heritability attributable to SNPs in the specified category divided by the proportion of total SNPs annotated to that category. The Bonferroni-corrected significance threshold was .05/56 annotations=.0009.
