To identify expression quantitative trait loci (eQTL) that have putative cis and trans [19] regulatory effects on the liver gene expression traits, we tested all expression traits for association with each of the SNPs in the analysis SNP set typed in the HLC. The strongest putative cis eQTL for a given expression trait was defined as the SNP most strongly associated with the expression trait over all of the SNPs typed within 1 megabase (Mb) of the transcription start or stop of the corresponding structural gene. The association p-values were adjusted to control for testing of multiple SNPs and expression traits using two different methods: (1) a highly conservative Bonferroni correction method to constrain the study-wise significance level, and (2) an empirical false discovery rate (FDR) method that constrains the overall rate of false positive events. For cis eQTL, we only test for associations to SNPs that are within 1 Mb of the annotated start or stop site of the corresponding structural gene. To achieve a study-wise significance level of 0.05, the Bonferroni adjusted p-value threshold was computed as ,
