Regions delineated using observed DNaseI data across 39 epigenomes, annotated with the 5-mark 15-state model based on observed data across 111 Roadmap reference epigenomes.
All coordinates are based on the Human hg19 genome assembly.
These putative regulatory regions have been delineated using DNaseI peak calls. Peak regions are combined into so called "peak islands", by merging similarly located regions across epigenomes.
Peak islands are then annotated/colored using the per-epigenome ChromHMM state calls of corresponding genomic bins.
We now distinguish three sets of regions: promoters, enhancers and 'dyadic' promoter/enhancer regions.
Visualization of these putative regulatory regions in the context of the chromatin states can be seen here.

DNaseI regions selected with -log10(p) >= 2

Promoters: 81,232 promoter regions (1.43958% of genome)

ChromHMM state calls (RData)
BED files per epigenome
Clustered with k=82, for a resolution of ~1k regions per cluster

Enhancers: 2,328,936 putative enhancer regions (12.6385% of genome)

ChromHMM state calls (RData)
BED files per epigenome
Clustered with k=226, for a resolution of ~10k regions per cluster

Dyadic: 129,960 dyadic promoter/enhancer regions (0.985296% of genome)

ChromHMM state calls (RData)
BED files per epigenome
Clustered with k=129, for a resolution of ~1k regions per cluster

For questions/comments, contact Wouter Meuleman (lastname at mit edu)