immune-specific enrichment could be because immune cells have better coverage, altered degradation, and/or a higher number of enhancers. We did not see a large enrichment of super-enhancers vs. regular enhancers; the estimates for enrichment were 1.8x (s.e. 0.2) for super-enhancers vs. 1.6x (s.e. 0.1) for regular enhancers from the same paper [19] (denoted “H3K27ac (Hnisz)” in Figure 4). We also did not see increased cell-type-specificity in super-enhancers (Supplementary Note). This lack of enrichment supports the hypothesis that super-enhancers may not play a much more important role in regulating transcription than regular enhancers [38]. For many annotations, there was also enrichment in the 500bp flanking regions (Supplementary Table 4); this could be because the boundaries are not well defined, because the boundaries of the regions are different in different individuals, or because unknown regulatory elements often appear close to known regulatory elements. Analyses stratified by derived allele frequency produced broadly similar results (Supplementary Table 6; see Online Methods).
