Question: Annotating SNPs for promoter and enhancer regions
gravatar for siddharth.sethi5
5.4 years ago by
Medical Research Council, Oxford, United Kingdom
siddharth.sethi5250 wrote:

Hi Everyone,

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.



snp promoter enhancer • 2.3k views
ADD COMMENTlink modified 5.4 years ago by Shicheng Guo8.5k • written 5.4 years ago by siddharth.sethi5250
gravatar for Emily_Ensembl
5.4 years ago by
Emily_Ensembl21k wrote:

Even if a regulatory feature is only active in one cell type, it's still relevant. Maybe it regulates a gene that's only active in one cell type, or a gene that is active in different pathways in different cell types. If you disrupt TF binding in that enhancer, you can still alter enhancer activity, still alter gene expression and still have a phenotypic effect.

ADD COMMENTlink written 5.4 years ago by Emily_Ensembl21k
gravatar for Shicheng Guo
5.4 years ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

Sid, This is the common problem of genetic variation based association study. Usually, we use PBMC as the DNA source to build the association between SNP, CNV with some specific phenotypes for which the disease source might be liver, lung or brain rather than PBMC itself. But we should clear that the genetic variance would bring light influence to our biological system in each tissue with long time (from your born), therefore, if we found some postive and significant assication between SNPs and phenotype, we need do our best to interpret the mechanism behind the association.    

ADD COMMENTlink written 5.4 years ago by Shicheng Guo8.5k
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