eQTL analysis identified no significant cis-eQTLs (q = 0.05); the smallest FDR-adjusted significance level for cis-eQTLs was q = 0.098 (not shown). There were 63 significant trans-eQTLs (q = 0.05; Additional File 4), and the most significant are shown in Table 4. A raw p-value of approximately 6 × 10-9 corresponded to q = 0.05. Even with a high 50% FDR cutoff, there were only 1,293 cis-eQTLs (of 1,468,327), or 0.09%, and 290,625 (of 507,010,655), or 0.06% trans-eQTLs. Although marginally significant (q = 0.049), the association between ZNF639 and TCF12 is included in Table 4 due to association of 3q26 with survival in this dataset [27] (Discussion). We did not perform gene ontology analysis of the eQTL experiment since there were no clear cis-eQTLs detected.
