Chunk #60 — Online Methods — eQTS mapping — Pruning SNPs and PGSs

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Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.

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To identify a set of independent SNPs, we conducted LD-based pruning as implemented in PLINK 1.976 with the setting --indep-pairwise 50 5 0.1. This yielded 4,586 uncorrelated SNPs (R2<0.1, GIANT 1000G p1v3 ALL).