EPIraction - an atlas of candidate enhancer-gene interactions in human tissues and cell lines.

Abstract

Enhancer-gene maps are essential to understand gene regulation. The identification of enhancers contributing to regulating a given gene, however, is challenging as they may lie far from the gene and act in a tissue-specific manner. Here we present EPIraction, an enhancer-gene atlas in the human genome. As H3K27ac is a typical mark of enhancer function, EPIraction relies on an exhaustive collection of 1,538 H3K27ac ChIP-Seq datasets. We used these data together with other epigenomic data to measure enhancer activity. To predict enhancer-gene interactions we first applied the conventional Activity By Contact algorithm to score enhancer-gene pairs in individual tissues. Then, we re-scored the interaction rewarding those present in biologically similar tissues. We used our predictions to annotate the candidate target genes for 1,664,956 SNPs from 3,693 UK Biobank and 760 FinnGen GWAS traits. The EPIraction predictions can be accessed through the portal at https://epiraction.crg.es. The portal can be employed to produce annotations for user-provided lists of SNPs or genomic intervals.