Expression quantitative trait loci (eQTL) were identified using a linear mixed model implemented in LIMIX 73,74. eQTLs were mapped in cis, considering a window of 1Mb around the gene start (as defined by Gencode v19 annotations). We modelled the genotype as a fixed effect, with population structure included as random effect. Population structure was modelled with a kinship matrix, calculated as the dot product of the genotypes in trans for each cis window (realized relationship).
