We have described the most comprehensive analysis to date of gene expression variation in human populations, and provide a detailed characterization of the genetic as well as the positional effects in the genome. This detailed analysis provides a robust and useful framework for the future analysis of gene expression variation in large cohorts with larger sample sizes but lower SNP densities and potentially multiple cell types. It will also greatly facilitate the interpretation and follow up of disease association studies by allowing the dissection of biological effects in regions that carry strong statistical signals of association. This and future studies will lead to a detailed map of functional variation in the human genome that will complement functional and variation studies towards the complete understanding of phenotypic variation in human populations.
