Question: How To Get Specific Encode Annotation For Snps?
3
gravatar for Nolwenn Lavielle
5.5 years ago by
Paris (France)
Nolwenn Lavielle90 wrote:

Hello everyone!

We work on GWAS, mainly, and we need to get informations about SNPs like:

  • is the SNP in a gene or up/downstream of a gene?
  • if the SNP is in a gene, is it in an intron, an exon?
  • is the SNP in a regulatory element (promoter, enhancer...)?
  • is the SNP in a binding motif (for which protein)?

I want to use ENCODE data for this but there is a lot of different data and many files.

Have you any advice for me which will help to get datas from them?

Which file do you use? Which tool (provided by UCSC or example of SQL request...)?

Do you use data other than ENCODE's (for example for the binding motifs)?

Thank you in advance.

Best regards, Nolwenn.

annotation snps motif encode • 3.0k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Nolwenn Lavielle90
3
gravatar for Pierre Lindenbaum
5.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

did you try:

haploreg: http://www.broadinstitute.org/mammals/haploreg/haploreg.php

or

regulomeDb: http://regulome.stanford.edu

?

ADD COMMENTlink written 5.5 years ago by Pierre Lindenbaum118k

Hi Pierre Lindenbaum

I also have some questions want to get your guidence. If i have genome resequencing SNPs located in intergenic region and I want to know whether are they in cis-regulatory element or not, what should i do? do you know some approaches to deal it ? 

ADD REPLYlink written 3.5 years ago by gzr31500

no, and you should ask this as a new question.

ADD REPLYlink written 3.5 years ago by Pierre Lindenbaum118k

Ok, Thanks Pierre Lindenbaum. I have asked it as a new question. How to locate the intergeneic SNPs in cis-regulatory element

ADD REPLYlink written 3.5 years ago by gzr31500
0
gravatar for Nolwenn Lavielle
5.5 years ago by
Paris (France)
Nolwenn Lavielle90 wrote:

I am also investigating on HaploReg but some of those datas seems to be calculated, in particular for the "Regulatory motif altered". I wonder if ENCODE provide this kind of informations too?

I had not try RegulomeDB, thanks for the reference! :)

ADD COMMENTlink written 5.5 years ago by Nolwenn Lavielle90
1

Please post this as a comment, not as an answer.

ADD REPLYlink written 5.5 years ago by PoGibas4.7k

I am confused. I was not sure if I had to comment or answer, now I am aware about this subtility. Thank you very much!

ADD REPLYlink written 5.5 years ago by Nolwenn Lavielle90
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