The Microarray eQTL study was used as a discovery cohort. Probe sets located within 1 Mb up and downstream of lung cancer SNPs were considered for cis-eQTL analyses. We have also explored a 5 Mb interval for lung cancer-associated SNPs not acting as lung eQTL within the 1 Mb window. The top eQTL association for that sentinel variant (or if contained multiple eQTL’s with P-value<0.0005 each was considered), this particular eQTL was then chosen and assessed specifically in the independent NCI and GTEx RNAseq eQTL datasets. Statistical significance was defined the eQTL surpassed a locus specific Bonferroni correlation in the discovery cohort (P-value=0.05/number of probes at that locus) and subsequently there was evidence for replication of the eQTL effect with that variant and gene within the validation cohorts (NCI/GTEx RNAseq).
