I have recently downloaded a melanocyte-specific FANTOM5 Human Enhancer Tracks (http://slidebase.binf.ku.dk/human_enhancers/presets). The fist 4 lines of the bed file looks like this:
chr1 1014834 1015095 chr1:1014834-1015095 0.034 . 1014858 1014859 0,0,0 2 1,213 0,48 chr1 2574343 2574764 chr1:2574343-2574764 0.012 . 2574704 2574705 0,0,0 2 332,29 0,392 chr1 6088225 6088518 chr1:6088225-6088518 0.03 . 6088327 6088328 0,0,0 2 85,173 0,120 chr1 7764543 7764931 chr1:7764543-7764931 0.02 . 7764716 7764717 0,0,0 2 133,174 0,214
Each predicted enhancer is described in BED12 format (columns 1-6 as chromosome, start coordinate, end coordinate, enhancer ID, score and strand) with two blocks denoting the merged regions of transcription initiation on the minus and plus strands. The thickStart and thickEnd columns denote the inferred mid position. The score column gives the maximum pooled expression of TCs used to construct each bidirectional loci.
I am interested in using this BED as custom annotation using VEP. However, I am not sure how to interpret the the BED file. How do I know if the variant I am looking at falls within an enhancer region? Can I see that from the given scores? If so, how would you interpret the scores?
Thank you very much in advance.