I am trying to annotate Snps and identify those snps which fall within promoter and enhancer regions. I am doing this using Mouse ENCODE data and have chromatin data for 23 TISSUES.
My question is, In how many tissues a SNP should be found to be annotated as enhancer/promoter to be considered as a regulatory snp ?
I find SNPs which fall in enhancer region only in 1 tissue. In other words, that region is annotated as enhancer only in one tissue, other tissues might have no annotation or other annotation. So, would this SNP (enhancer in only 1 tissue) would be interesting/important or it can be incorrect or low confidence annotation and should be ignored?
Also, how similar these chromatin profiles are between tissues ?
Would appreciate any kind of help.