To map the underlying common, genetic effect of transcript levels, we performed global cis-eQTL mapping associating the 23,596 expression traits with imputed HapMap2 genotypes in a linear mixed (polygenic) model followed by a score test taking the relatedness into account (Supplementary Fig 2). cis-eQTLs were called with a per tissue FDR of 1%, which corresponds to P <5.0×10−5 in adipose, P < 7.8×10−5 in LCL and P < 3.8×10−5 in skin tissue, respectively. Across all transcripts, we detected an abundance of cis-eQTLs per tissue (Nadipose=3529, NLCL=4625, Nskin=2796, Supplementary Table 3) with 14%, 17% and 10% of transcripts with a cis-eQTL in adipose, LCL and skin tissue, respectively having more than one independent cis-eQTLs. For these transcripts associated with at least one cis-variant, the average h2 estimates are 0.31, 0.25 and 0.21 in adipose, LCL and skin tissue, respectively. The probability of detecting large effect sized cis-eQTLs across tissues increases with heritability as shown by average h2 estimates of transcripts associated with a cis-variant at P<5×10-8 where a maximum average h2 seen in adipose tissue is 0.38.
