Hi,

This is actually not a straightforward question. One gene can be regulated by multiple enhancers and one enhancer can regulate multiple genes. Furthermore, enhancer activity is oftentimes cell-type specific.

The only way to really identify whether a given region is a bona fide enhancer for your gene of interest is through experimental validation (e.g. CRISPR perturbation).

To identify candidate enhancers, typically H3K27ac ChIP-Seq and/or ATAC-seq (chromatin accessibility) signal is used. To predict which gene(s) an enhancer is associated with, many studies simply employ a distance threshold (e.g. the gene(s) for which the enhancer is within 50 kb or 100 kb of their promoter or TSS) or simply conservatively select the closest gene. Such predictions perform OK, but they are far from ideal.

In any case, many enhancer databases have been developed based off predictions like these:

• HACER: http://bioinfo.vanderbilt.edu/AE/HACER/
• EnhancerAtlas: http://www.enhanceratlas.org/indexv2.php
• Vista Enhancer browser: https://enhancer.lbl.gov/

And superenhancer databases too:

• dbSUPER: http://asntech.org/dbsuper/index.php

However, again, these just give you candidate enhancer-gene associations that are based off prediction models that are OK but not great. Experimental validation remains necessary.

Better prediction models are still actively being developed; the most recent enhancer-gene association prediction model, which integrates chromatin accessibility, H3K27ac signal, and Hi-C contact data, was just published just last month: Fulco, Nasser, et al. Nature Genetics, 2019, https://www.ncbi.nlm.nih.gov/pubmed/31784727 - This paper (based mainly on work done at the Broad Institute) is worth checking out just to give you a better idea of enhancer-gene associations and the challenges of identifying them.