How to find SNPs in Promoter or Enhancer region?

Question

[1078256104]

I want to study a gene ,but how can i find SNPs in the potential regulatory motifs such as promoter or enhancer in the gene region?

Hope you can help me,many thanks!

Answer 1

[Emily]

The Ensembl VEP will report if any variants have fallen within any promoters or enhancers predicted from ENCODE/Roadmap Epigenomics data by our regulatory build, and if they've fallen in in TF motifs and change the motif strength.

[GouthamAtla]

Great information.

Answer 2

[rob234king]

use snpeff to predict effect of snp, set maximum upstream length in snpeff first though as 1000bp is default I think, and filter for effect for upstream of gene. Then look at them in more detail. There may be a specific tool to do this but don't know it. Would be interested if someone has a more automated method if promoters are not annotated already..