active enhancers [19]; and enhancers with balanced bidirectional capped transcripts identified using cap analysis of gene expression in the FANTOM5 panel of samples, which we call FANTOM5 enhancers [23]. For the histone marks and other annotations that differ among cell types, we combined the different cell types into a single annotation for the full baseline model by taking a union (except for Repressed, where we took an intersection). To prevent our estimates from being biased upwards by enrichment in nearby regions [14], we also included 500bp windows around each functional category in the full baseline model, as well as 100bp windows around ChIP-seq peaks when appropriate (see Online Methods). This yielded a total of 53 (overlapping) functional categories in the full baseline model, including a category containing all SNPs.
