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PostPosted: Fri Aug 23, 2013 4:27 am 
Hello GREAT team!

I currently have a list of SNPs and I would like to see which genes are likely to be affected by these SNPs. Is GREAT suitable for this? I loaded a list of SNPs (with whole genome background) and eventually got to the genomic region - gene association table. Is this an indication of the genes that are potentially affected by the SNPs?

I donĀ“t have a lot of bioinformatics experience, so I am rather desperate!

Thanx :)
Michelle
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PostPosted: Fri Aug 23, 2013 6:19 pm 
Site Admin
Hi Michelle,

GREAT defines gene regulatory domains as per http://bejerano.stanford.edu/help/display/GREAT/Association+Rules. The gene association table shows the (SNP, gene) pairings based on SNPs that fall into a gene's regulatory domain.

If you believe your SNPs are occurring in cis-regulatory elements, then it is indeed possible that those genes are are potentially affected by the SNPs in their regulatory domains.

Thanks,
Bejerano Team
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