Genotyping was performed using Affymetrix 6.0 arrays. After filtering out SNPs poorly performing or having a minor allele frequency <0.01, 675,350 SNPs were kept for further analyses. All associations between SNPs and expression traits with a P-value <10−5 (n>225,000) were stored in the “GHS_Express” database (“GHS_Express” is available online, see Methods S1 ). At a study-wise threshold of significance correcting for the number of SNPs and expressions (P<5.78×10−12), 37,403 associations, involving 29,912 SNPs and 2,745 expression traits (referred to as eSNPs and eQTLs, respectively), were identified ( Table 2 ). The median number of eSNPs by eQTL was 11 with an interquartile range of 4 to 26. Owing to its large sample size, the study had an 80% power to detect a SNP effect accounting for 4% or more of the variability (R2) of any expression trait. Among the 2,745 significant eQTLs, the R2 observed for the best eSNP varied from 3.1% to >80% with a median of 7.7%. For 290 eQTLs, the R2 was greater than 25%.
