Super-enhancers are large clusters of transcriptional enhancers that drive 
expression of genes that define cell identity. Improved understanding of the 
roles that super-enhancers play in biology would be afforded by knowing the 
constellation of factors that constitute these domains and by identifying 
super-enhancers across the spectrum of human cell types. We describe here the 
population of transcription factors, cofactors, chromatin regulators, and 
transcription apparatus occupying super-enhancers in embryonic stem cells and 
evidence that super-enhancers are highly transcribed. We produce a catalog of 
super-enhancers in a broad range of human cell types and find that 
super-enhancers associate with genes that control and define the biology of 
these cells. Interestingly, disease-associated variation is especially enriched 
in the super-enhancers of disease-relevant cell types. Furthermore, we find that 
cancer cells generate super-enhancers at oncogenes and other genes important in 
tumor pathogenesis. Thus, super-enhancers play key roles in human cell identity 
in health and in disease.