Fig. 4

Enhancers have different levels of enrichment with functional attributes. (a) Enhancer sets vary in their degree of evolutionary conservation. Each point represents the enrichment (fold change compared to randomly shuffled regions) for overlap between a conserved element (combined primate and vertebrate PhastCons) and each enhancer set. Methods based on transcriptional assays and TF binding profiles (GRO-cap, FANTOM, p300, and Yip12) are the most enriched for conserved elements, while sets based on histone modification data alone are among the least enriched. (b) GWAS SNP enrichment among all enhancer sets for each biological context. All sets are significantly enriched, except FANTOM in K562 and liver contexts due to small sample size. (c) GTEx eQTL enrichment among all enhancer sets for each biological context. Transparent points indicate nonsignificant enrichment (p > 0.05)