SNP annotation with TFBS and histone marks

Question

[LNA]

Hi,

I have to annotate a list of SNPs with information about transcription factor binding sites and histone marks. I found data for download on the UCSC webpage, but I'm hoping for a more straightforward way to do this. In another post someone recommended using the Enseml VEP for this task. Is the VEP the best way to do this? Would the outcome be very different from the UCSC annotation?

When trying VEP I found "TF_binding_site" entries and "open_chromatin_region" entries in the output list. Is there any more information about histone marks that I missed? Do I have to select some additional tools for the query that I missed?

Thank you for your help!

Answer 1

[Emily]

The VEP will map your variants to TF motifs certainly, but there's currently no output that will give that will map to specific histone modifications. It will map your variants to regulatory features, such as promoters and enhancers, which are predicted based on TF binding, open chromatin and histone modifications (see Ensembl regulatory build), which you can then explore to see the histone mods at those loci in different cell types.

I wondered if RegulomeDB might get you what you need, but they also don't mention histone mods.