The eQTL analysis was done separately for each tissue, as previously described 11. Within each tissue, twins from the same pair were separated by id in two samples analyzed independently. Related individuals (sister pairs) within a twin set were also removed. This separation resulted in the following sample size for adipose, LCL and skin respectively: Twin 1 (390, 340 and 337) and Twin 2 (384, 338 and 328). For each of the twin–by-tissue sets, associations between genotypes and normalized expression values were conducted using Spearman Rank Correlation (SRC). Age and experimental batch were included as cofactors in the adipose and LCL analysis, and age, batch and sample processing in the skin analysis. We considered a window of <1MB from the TSS for testing SNPs in cis. cis-eQTLs were filtered at a nominal SRC P < 2.5×10−6 corresponding to a 10-3 permutation threshold 11. We contrasted the eQTLs (same SNP-probe combination) and expression fold change (difference in mean expression of homozygous genotypic classes) between twin sets of the same tissue followed by inter-tissue comparison of the same twins (e.g. Twin1 LCL vs. Twin2 LCL, Twin1 LCL vs. Twin1 adipose, Twin1 LCL vs. Twin1 skin).
