We analyzed the same 48 diseases and traits using stratified LD score regression7 in conjunction with chromatin data from the Roadmap Epigenomics and ENCODE projects1,2 (see URLs) instead of gene expression data, with three goals: (1) to validate the results from our analysis of gene expression data using a different type of data from an independent source, (2) to identify new enrichments using chromatin data that we did not observe using gene expression data, and (3) to compare enrichments from the two types of data. The ENCODE data we used was from a subproject called EN-TEx, which includes epigenetic data on a set of tissues that match a subset of the tissues from the GTEx project but are from different donors. In total, we analyzed 489 tissue-specific chromatin-based annotations from peaks for six epigenetic marks (Online Methods).
