A primary goal of the GTEx project is to identify eQTLs for all genes for a range of human tissues. Past studies, hampered by the difficulties of obtaining human tissue samples, have typically examined no more than three tissues (8, 20). Although our pilot sample sizes are modest for eQTL discovery, the breadth of tissues provides an opportunity to assess differential eQTL discovery among tissues. Because of our small sample sizes, we primarily examined eQTLs that act in cis to the gene (cis-eQTLs; see box S1), as the expected effect size of trans-eQTLs (box S1) is too low to be efficiently detected at this time. We calculated cis-eQTLs separately for each of the nine tissues with sufficient sample sizes (>80 donors) for all SNPs within ±1 Mb of the transcriptional start site (TSS) of each gene (14). Significance correlations between genotypes and gene expression levels were determined by linear regression on quantile normalized gene-level expression values, after correction for known and inferred technical covariates (fig. S8) (14), using Matrix eQTL (21). To obtain gene-specific significance levels while correcting for testing
