I am not able to understand your question properly, but if you mean annotating the peaks obtained from ChIP-Seq for histone modification study. Then you can try using annotatePeaks.pl which is a simple perl script, a part of HOMER package. You basically need 3 files for running it:
Peak bed file reference genome fasta file reference genome annotation (gtf/gff) file
And command goes like this:
perl annotatePeaks.pl sample_peak.bed Genome.fasta -gft genome.gft >homer_annotation.txt
It basically gives you "Distance to the nearest TSS".
For other alternatives, you can go through this post.