LD threshold r2 >0.2) were excluded from analysis. Similarly, we removed 24,170 SNP-transcript combinations with an InDel overlapping with a transcript probe, according to the Database of Genomic Variants (version 10, November 2010) [35]. There were 3,541,781 possible SNP-transcript combinations in cis left for analysis. The number of possible combinations in cis was used for Benjamini-Hochberg false discovery rate (FDR) calculations. Significant cis effects were those SNP-transcript pairs that had significant p values at an FDR of 5% after 10,000 permutations. Permutations were performed swapping case/controls labels so that each subject is assigned the genotype vector of another random subject, while the expression matrix is unchanged. This prevents the underestimation of the null distribution, thereby preventing the detection of false-positive eQTLs, as described previously [36]. Analyses were performed in PLINK [28] and R (2009, The R Foundation for Statistical Computing).
