Cap Analysis of Gene Expression5 (CAGE), we show that enhancer activity can be detected through the presence of balanced bidirectional capped transcripts, enabling the identification of enhancers from small primary cell populations. Based upon the FANTOM5 CAGE expression atlas encompassing 432 primary cell, 135 tissue and 241 cell line samples from human6, we identify 43,011 enhancer candidates and characterize their activity across the majority of human cell types and tissues. The resulting catalogue of transcribed enhancers enables classification of ubiquitous and cell type-specific enhancers, modeling of physical interactions between multiple enhancers and TSSs, and identification of potential disease-associated regulatory single nucleotide polymorphisms (SNPs).
