Our analysis goes beyond the mere detection of cis regulatory effects. We have performed to our knowledge, the most comprehensive analysis to date of the properties of the cis association signals, and we have systematically described characteristics of the expression data. Together these analyses provide us with confidence in the detected signals. In addition, we have demonstrated that the detected association signals replicate very well across populations, even though the populations are quite divergent and the sample sizes are small. We also detect the effect of population differentiation on gene expression. In this respect, we confirm what has been previously documented in smaller scale studies 16,28; Among-population allele frequency differences exist and provide a framework for the study of phenotypic differences among populations.
