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Background  Localising regulatory variants that control gene expression is a challenge for genome research. Several studies have recently identified non-coding polymorphisms associated with inter-individual differences in gene expression. These approaches rely on the identification of signals of association against a background of variation due to other genetic and environmental factors. A complementary approach is to use an Allele-Specific Expression (ASE) assay, which is more robust to the effects of environmental variation and  trans -acting genetic factors.    Methodology/Principal Findings  Here we apply an ASE method which utilises heterozygosity within an individual to compare expression of the two alleles of a gene in a single cell. We used individuals from three HapMap population groups and analysed the allelic expression of genes with  cis -regulatory regions previously identified using total gene expression studies. We were able to replicate the results in five of the six genes tested, and refined the  cis - associated regions to a small number of variants. We also showed that by using multi-populations it is possible to refine the associated  cis -effect DNA regions.    Conclusions/Significance  We discuss the efficacy and drawbacks of both total gene expression and ASE approaches in the discovery of  cis -acting variants. We show that the ASE approach has significant advantages as it is a cleaner representation of  cis -acting effects. We also discuss the implication of using different populations to map  cis -acting regions and the importance of finding regulatory variants which contribute to human phenotypic variation.

Validating Discovered Cis-Acting Regulatory Genetic Variants: Application of an Allele Specific Expression Approach to HapMap Populations