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Tag Snp, Independent Gwas, Eqtl Results

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?

Thanks.

snp gwas eqtl
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written by Zhenyu Zhang Zhenyu Zhang

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.

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written by Maxime Lamontagne Maxime Lamontagne

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

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written by Zhenyu Zhang Zhenyu Zhang

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