The robustness of the 3,430 associations to environmental sources of variance and population structure was further evaluated by fitting two additional linear trend models to the data. The first included location, gender and the interaction between them. The second included two measures of ethnicity (the first three genotype eigenvectors and a four-way categorical ethnicity cluster: see methods), a matrix of relatedness based on an identity by descent measure27, as well as gender interactions with ethnicity cluster and genotype. Figures 5a and 5b show the Manhattan plot of associations by chromosomal location for the second of these models, and the cis-trans plot of target against eSNP location, respectively. Figure 5c and Supplementary Fig. 7 online show that the logarithm of the genotype significance term is highly correlated (r > 0.95) between both of these models and the original correlation test. Furthermore, Figure 5d shows that there is no evidence for significant genotype-by-location interactions in any of the association trend tests. Neither the ethnicity nor the relatedness variance components explain an appreciable amount of the expression variation for any of the transcripts (Supplementary Fig. 8 online).
