Our estimated enrichments were higher for the chromatin-based annotations than for the gene expression-based annotations, but the gene expression-based annotations are larger and have less LD to the rest of the genome. Some chromatin marks tend to be more cell type-specific than overall gene expression, but our specifically expressed gene sets have low correlation across tissues (Figure S17). There were two instances in which we had gene expression and chromatin data on the same set of tissues/cell types, and we compared the P-values in our analyses of these data sets. First, we compared our results from GTEx (gene expression) and EN-TEx (chromatin) for the tissues shared between these two data sets in the multiple-tissue analysis, and we found that the two data sets had comparable distributions of P-values (Figure S4). On the other hand, the hematopoietic data set that we analyzed64 had matched ATAC-seq and RNA-seq data, and while our analysis of the ATAC-seq peaks lead to significant enrichments for many traits (Figure 5, Table S10), the RNA-seq data set yielded only a single enrichment for a single trait (Table S16).
