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.