Super-enhancers and stretch enhancers represent classes of transcriptional 
enhancers that have been shown to control the expression of cell identity genes 
and carry disease- and trait-associated variants. Specifically, super-enhancers 
are clusters of enhancers defined based on the binding occupancy of master 
transcription factors, chromatin regulators, or chromatin marks, while stretch 
enhancers are large chromatin-defined regulatory regions of at least 3,000 base 
pairs. Several studies have characterized these regulatory regions in numerous 
cell types and tissues to decipher their functional importance. However, the 
differences and similarities between these regulatory regions have not been 
fully assessed. We integrated genomic, epigenomic, and transcriptomic data from 
ten human cell types to perform a comparative analysis of super and stretch 
enhancers with respect to their chromatin profiles, cell type-specificity, and 
ability to control gene expression. We found that stretch enhancers are more 
abundant, more distal to transcription start sites, cover twice as much the 
genome, and are significantly less conserved than super-enhancers. In contrast, 
super-enhancers are significantly more enriched for active chromatin marks and 
cohesin complex, and more transcriptionally active than stretch enhancers. 
Importantly, a vast majority of super-enhancers (85%) overlap with only a small 
subset of stretch enhancers (13%), which are enriched for cell type-specific 
biological functions, and control cell identity genes. These results suggest 
that super-enhancers are transcriptionally more active and cell type-specific 
than stretch enhancers, and importantly, most of the stretch enhancers that are 
distinct from super-enhancers do not show an association with cell identity 
genes, are less active, and more likely to be poised enhancers.