Rare variants linkage disequilibrium
Entering edit mode
6 months ago
reds.nik ▴ 40

Hi everyone,

I found a burden of rare variants within an haplotype block associated with a trait of interest. Given that the associated region is surrounded by common eQTL variants, I would like to show that these rare variants may be eQTLs themselves, being, for example, in strong linkage disequilibrium (LD) with known common eQTLs from databases (I don't have gene expression data for my dataset). I know that standard ways to report LD include R2 and D' which, however, make more sense when comparing common variants or rare variants separately. On the contrary, R2 and D' are not really meaningful when comparing rare variants with common variants. Is there any good strategy to show that some rare genetic variants are capturing some common reported eQTLs signals?

snp linkage disequilibrium rare variants • 192 views

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