I want to identify a list of accessible genes in a DNase-seq experiment. I downloaded the alignment file `ENCFF001CTZ.bam` from [Encode][1]. I performed peak calling by using macs1.4 and obtained a peaks.bed file containing coordinates of peaks. Next, I performed peak annotation by Homer using `annotatePeaks.pl`. The Final annotation file I obtained contains following columns:

    "Peak_ID" "Chr" "Start" "End" "Strand" "Peak.Score" "Focus.Ratio.Region.Size" "Annotation" "Detailed.Annotation" "Distance.to.TSS" "Nearest.PromoterID" "Entrez.ID" "Nearest.Unigene" "Nearest.Refseq" "Nearest.Ensembl" "Gene.Name" "Gene.Alias" "Gene.Description" "Gene.Type"

A screenshot of Annotation_File from Homer is [here][2].

**QUESTION:** How I can finally obtain a list of genes which I can say are accessible? Do I need to only take genes for whose the column '*Annotation*' tells me that region is near to '*promoter-TSS*' or I can also take those which are '*Intergenic*' or so?

What information this (that a gene's intergenic region or intron is accessible) can provide?

 [1]: https://www.encodeproject.org/experiments/ENCSR000EMT/
 [2]: https://www.dropbox.com/s/0v1iflhcmbtu01l/Screenshot%20from%202015-12-08%2017%3A22%3A44.png?dl=0
Strictly speaking, any DNAseI HS site that overlaps a gene would be an "accessible gene".

But I'm guessing that you're looking for a transcribed gene(?); a gene that is accessible to PolII? If that's the case, you want the promoter-TSS overlaps.

DNaseI sites that sit elsewhere in the genome could be enhancers, but you would need more information to define these. Or they could be virtually anything else. I'm not aware of any studies that have tried to characterise the protein profiles associated with HS sites at non-promoter sites.