One of the fundamental questions of human population genetics is the extent to which human populations from around the world differ from one another. Population differentiation can be seen from the perspective of history, where neutral DNA sequence variation is used to reconstruct the relationships between populations given models of demography, migration, and genetic drift. The recent revolution of experimental approaches that address genome function has allowed the characterization of population differentiation with respect to variants that alter genome function. To date, two types of functional variants have attracted the most attention (i) variants that alter protein coding sequence (non-synonymous variants), and (ii) variants that are associated with levels of gene expression, i.e., regulatory variants that are also referred to as eQTLs (expression Quantitative Trait Loci). While there have been extensive studies of human population differentiation with respect to protein coding variants [1], [2], little is known about the degree of population differentiation of regulatory variants, either for those with regulatory effects on nearby genes (cis-eQTLs) or those acting over longer genomic distances (trans-eQTLs). This deficit of knowledge needs to
