Question: How to find SNPs in Promoter or Enhancer region?
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gravatar for 1078256104
4.6 years ago by
10782561040
China
10782561040 wrote:

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!

snp promoter • 2.7k views
ADD COMMENTlink modified 4.6 years ago by Emily_Ensembl21k • written 4.6 years ago by 10782561040
2
gravatar for Emily_Ensembl
4.6 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

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.

ADD COMMENTlink written 4.6 years ago by Emily_Ensembl21k

Great information.

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.6 years ago by geek_y11k
0
gravatar for rob234king
4.6 years ago by
rob234king600
UK/Harpenden/Rothamsted Research
rob234king600 wrote:

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..

ADD COMMENTlink written 4.6 years ago by rob234king600
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