If you have a TSS or alternative epigenomics annotation file of interest (eg from modENCODE) in BED format you can use Bedtools or Bedops to intersect overlapping peaks.

You could get TSS from gene annotations specific to your reference genome, e.g.:

A: Table browser +/- 2Kb of TSS export

Once you have that, you can find set intersections via something like:

$ bedops --element-of 1 peaks.bed tss.bed > peaks_that_overlap_tss.bed

If you'd rather get a calculation of which peaks overlap which TSS, specifically:

$ bedmap --echo --echo-map tss.bed peaks.bed > tss_with_associated_peaks.bed

The difference between bedops and bedmap, very generally, is that bedops does set and interval operations (intersect, difference, etc.), while bedmap does associations between genomic elements in sets ("mapping").