Thursday, April 19, 2007

How to find the important SNP   posted by amnestic @ 4/19/2007 08:48:00 PM

There is a gene I care about carrying a SNP associated with a phenotype I care about. Unfortunately, that SNP is intronic, and if it has an effect the prediction isn't obvious. I would like very much to find a list of SNPs in significant LD with this one, but I am finding the HapMap/Mart impenetrable. In this article, Navigating the HapMap, I got a hint of hope:
Alternatively, one might use the SNP filter function to highlight other SNPs that are in LD with a specific list of SNPs of interest (e.g. SNPs associated in a study). This enables the user to identify all SNPs in LD with an associated SNP to allow functional analysis to identify putative causal SNPs for further analysis in the lab.

I can't find this option. Any helpful hints?