GTEx V6 analysis results are based on genotypes imputed to 1000 Genomes (1KG) Phase I version 3. Thus, significant results could be LD-filtered using Phase I data. However, to make use of the larger sample size in later projects, 1KG Phase 3 genotypes will be used.
Create region file to use with bcftools for LD.
Filter 1KG genotypes to only include EUR unrelated individuals and eQTL region.
Run PLINK clump command using default settings, but might want to change with different nominal significance thresholds.
PLINK clump command identifies 8 independent eSNPs in the region.
Next step, extract independent eSNPs from individual level genotype data, build MR risk score, evaluate for association with survival time.