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Common genetic variants account for differences in gene expression among ethnic groups

Nature Genetics volume 39, pages 226231 (2007) | Download Citation



Variation in DNA sequence contributes to individual differences in quantitative traits, but in humans the specific sequence variants are known for very few traits. We characterized variation in gene expression in cells from individuals belonging to three major population groups. This quantitative phenotype differs significantly between European-derived and Asian-derived populations for 1,097 of 4,197 genes tested. For the phenotypes with the strongest evidence of cis determinants, most of the variation is due to allele frequency differences at cis-linked regulators. The results show that specific genetic variation among populations contributes appreciably to differences in gene expression phenotypes. Populations differ in prevalence of many complex genetic diseases, such as diabetes and cardiovascular disease. As some of these are probably influenced by the level of gene expression, our results suggest that allele frequency differences at regulatory polymorphisms also account for some population differences in prevalence of complex diseases.

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We thank T. Weber for carrying out the microarray hybridizations, V. Mancuso for processing samples and data analysis and H. H. Kazazian and K. Ewens for comments on the manuscript. This work was supported by US National Institutes of Health grants (to R.S.S, V.G.C) and by the W.W. Smith Chair (V.G.C.).

Author information


  1. Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

    • Richard S Spielman
    •  & Vivian G Cheung
  2. Department of Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

    • Laurel A Bastone
  3. The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.

    • Joshua T Burdick
    • , Michael Morley
    •  & Vivian G Cheung
  4. Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

    • Warren J Ewens
  5. Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

    • Vivian G Cheung


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Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Richard S Spielman or Vivian G Cheung.

Supplementary information

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  1. 1.

    Supplementary Table 1

    Genes whose expression differs significantly between CEU and CHB+JPT samples.

  2. 2.

    Supplementary Table 2

    Four genes with evidence for differences in mean expression between CEU and CHB+JPT due to different regulatory mechanisms.

  3. 3.

    Supplementary Table 3

    Four genes with evidence for differences in mean expression between CEU and CHB+JPT due to different regulatory mechanisms.

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