Using a common set of markers from 1000 Genomes SNP imputation, the MRCA (Affymetrix) and the MRCE (Illumina) data together identified genome-wide significant (Benjamini and Hochberg FDR < 5%) (Benjamini and Hochberg 1995) eQTLs for transcripts from 13,661 autosomal genes. We found shared eQTLs for 2483 genes in both MRCA and MRCE data set, while 4819 genes were only mapped by the MRCA data and 6358 genes were specific to MRCE data (Supplemental Fig. 5). For particular gene–SNP associations, there were 136,466 gene–SNP pairs mapped in both MRCA and MRCE, while 416,952 were specific to MRCA and 492,861 were specific to MRCE.
