SEs show significant enrichment of GWAS SNPs associated with diseases or quantitative in a cell-specific manner. Positions of index and tightly linked (r2 ≥ 0.8) SNPs for different diseases or traits (y-axis) are overlapped with those of DHSs within SEs, non-DHSs with SEs, and motif sites in either DHSs or non-DHSs within SEs for each cell type (x-axis). Only motifs from the cell-specific motif sets used to generate the motif density tracks in Figure 4 are considered for each cell type. Motif sites were identified with FIMO at the default threshold of p < 10−4. Text in the boxes indicates the number of overlapping SNP loci in each cell type. Shading indicates the significance of SNP locus enrichment relative to a null distribution (“Methods”). Only SNPs that meet the genome-wide significance threshold (p < 5 × 10−8) are considered.