We have performed a comprehensive study of cis- regulatory variation in a single cell type of individuals comprising a diverse set of eight human populations. The analysis of the genetics of nearly 20,000 gene expression phenotypes in such a number of human population samples allows us to identify large numbers of functionally variable regulatory regions in the human genome, as well as to estimate the degree of an aspect of functional variation that has not been assessed before. We find that at least 20% of the genes tested in our analysis have a common cis-eQTL in at least one population, and we detect extensive sharing of eQTLs across human populations even with fluctuations in allele frequencies, while there is also substantial non-genetic variance in gene expression levels. Overall, our data show that across all populations, there is an enrichment among population differentiated genes for those genes involved in regulatory function, while each population has unique sets of sets of genes, and categories of gene function, whose expression levels differentiate that population.
