Question: Tag Snp, Independent Gwas, Eqtl Results
gravatar for Zhenyu Zhang
6.9 years ago by
Zhenyu Zhang270
United States
Zhenyu Zhang270 wrote:

I seems many gwas/eqtl results does not report all associations, but only those independent features. I mean, if some SNPs are correlated, only one was reported. My questions are: 1. Is it called tagging SNP? 2. How is this SNP selected? 3. When comparing multiple eQTL results with different independent SNP sets, how people do it?


gwas eqtl snp • 1.7k views
ADD COMMENTlink written 6.9 years ago by Zhenyu Zhang270

2: Probably with sliding window.

1: Yes and No. Yes because they use tag SNPs in each "window". No because they need to use region of predefined size and some genes could be longer than these regions. Two SNPs in two consecutives windows could be in LD.

3: They probably look in the 1000 Genomes Project or HapMap to find SNPs in LD with their SNPs. After that, they look in the eQTLs results if these SNPs are there.

ADD REPLYlink modified 6.9 years ago • written 6.9 years ago by Maxime Lamontagne2.2k

Thanks a lot. Regarding sliding window, do you have a suggested paper/protocol/package that I could follow?

ADD REPLYlink written 6.9 years ago by Zhenyu Zhang270
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1862 users visited in the last hour