High-density single-nucleotide polymorphism maps of the human genome

Raymond D. Miller, Michael S. Phillips, Inho Jo, Miriam A. Donaldson, Joel F. Studebaker, Nicholas Addleman, Steven V. Alfisi, Wendy M. Ankener, Hamid A. Bhatti, Chad E. Callahan, Benjamin J. Carey, Cheryl L. Conley, Justin M. Cyr, Vram Derohannessian, Rachel A. Donaldson, Carolina Elosua, Stacey E. Ford, Angela M. Forman, Craig A. Gelfand, Nicole M. GreccoSusan M. Gutendorf, Cricket R. Hock, Mark J. Hozza, Soyoung Hur, Mi In Sun, Diana L. Jackson, Ahn Jo Sangmee, Sung Chul Jung, Sook Kim, Kuchan Kimm, Ellen F. Kloss, Daniel C. Koboldt, Jennifer M. Kuebler, Feng Shen Kuo, Jessica A. Lathrop, Jong Keuk Lee, Kathy L. Leis, Stephanie A. Livingston, Elizabeth G. Lovins, Maria L. Lundy, Sima Maggan, Matthew Minton, Michael A. Mockler, David W. Morris, Eric P. Nachtman, Bermseok Oh, Chan Park, Chang Wook Park, Nicholas Pavelka, Adrienne B. Perkins, Stephanie L. Restine, Ravi Sachidanandam, Andrew J. Reinhart, Kathryn E. Scott, Gira J. Shah, Jatana M. Tate, Shobha A. Varde, Amy Walters, J. Rebecca White, Yeon Kyeong Yoo, Jong Eun Lee, Michael T. Boyce-Jacino, Pui Yan Kwok

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans as part of The SNP Consortium's Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency ≥10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the several percentage point allele frequency differences among the closely related Korean, Japanese, and Chinese populations suggest caution in using mixtures of well-established populations for case-control genetic studies of complex traits. We estimate that ∼7% of these SNPs are private SNPs with minor allele frequencies <1%. A useful set of characterized SNPs with large allele frequency differences between populations (>60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available.

Original languageEnglish
Pages (from-to)117-126
Number of pages10
Issue number2
StatePublished - Aug 2005


  • Complex disease variation search
  • Human variation
  • Korean population
  • Pooled sequencing
  • SNP
  • Single-base primer extension
  • The SNP Consortium


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