How To Get Specific Encode Annotation For Snps?

Question

[Nolwenn Lavielle]

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.

Answer 1

[Pierre Lindenbaum]

did you try:

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

or

regulomeDb: http://regulome.stanford.edu

?

[gzr3150]

Hi Pierre Lindenbaum

I also have some questions want to get your guidance. If I have genome resequencing SNPs located in intergenic regions 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?

[Pierre Lindenbaum]

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

[gzr3150]

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

Answer 2

[Nolwenn Lavielle]

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! :)

[PoGibas]

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

[Nolwenn Lavielle]

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!