Detected eQTLs in 1,469 genetical genomics samples for 289,044 common SNPs and for 1,167 trait-associated SNPs.

For 289,044 SNPs, present on the commonly used Illumina HumanHap300 platform, the false discovery rate (FDR) was controlled at 0.05 for both cis- and trans-eQTLs. For the analysis of 1,167 successfully imputed SNPs that have been found associated with a quantitative trait or disease the FDR was controlled at 0.05 for the cis- and trans-eQTLs. We also performed a trans-eQTL analysis for these SNPs while controlling the FDR at 0.50 to generate more hypotheses. The number of unique genes was determined using Ensembl 52 (NCBI 36.3 release).