Can someone help me to identify potential enhancers located within the introns of genes within the human genome: chr22:30,000,000-35,000,000 (2009 assembly, hg19) that are differentially active in HUVECs vs NHLFs. I'm not sure what track to use in the UCSC browser or how to find data in the introns only.
Perhaps you can find useful information in the FANTOM5 project's transcribed enhancers atlas? Here is a link to your region of interest in our ZENBU genome browser view. The track of interest is called _FANTOM5 Human permissive enhancers phase 1 and 2_.
Another valuable resource is the Roadmap epigenomics browser: http://egg2.wustl.edu/roadmap/web_portal/
We use H3K4me1 and H3K27ac overlaps as putative enhancer marks. You can use Bedtools IntersectBed to overlap the two. You can download the histone peaks from UCSC Genome Browser, then use HOMER annotation to annotate the peaks and filter for introns.
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