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A second generation human haplotype map of over 3.1 million SNPs

Nature volume 449, pages 851–861 (2007)Cite this article

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Abstract

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10–30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.

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Figure 1: SNP density in the Phase II HapMap.
Figure 2: Haplotype structure and recombination rate estimates from the Phase II HapMap.
Figure 3: The extent of recent co-ancestry among HapMap individuals.
Figure 4: Properties of untaggable SNPs.
Figure 5: Recombination rates around genes.
Figure 6: Properties of non-synonymous and synonymous SNPs.

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  • 18 January 2008

    Co-author Todd A. Johnson's name was inadvertently omitted from the list of RIKEN authors in the HTML version of the paper only. This was corrected on 18 January 2008.

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Acknowledgements

We thank many people who contributed to this project: all members of the genotyping laboratory and the sample, primer, bioinformatics, data quality and IT groups at Perlegen Sciences for technical and infrastructural support; J. Beck, C. Beiswanger, D. Coppock, A. Leach, J. Mintzer and L. Toji for transforming the Yoruba, Japanese and Han Chinese samples, distributing the DNA and cell lines, storing the samples for use in future research, and producing the community newsletters and reports; J. Greenberg and R. Anderson for providing funding and support for cell line transformation and storage in the NIGMS Human Genetic Cell Repository at the Coriell Institute; T. Dibling, T. Ishikura, S. Kanazawa, S. Mizusawa and S. Saito for help with genotyping; C. Hind and A. Moghadam for technical support in genotyping and all members of the subcloning and sequencing teams at the Wellcome Trust Sanger Institute; X. Ke for help with data analysis; Oxford E-Science Centre for provision of high-performance computing resources; H. Chen, W. Chen, L. Deng, Y. Dong, C. Fu, L. Gao, H. Geng, J. Geng, M. He, H. Li, H. Li, S. Li, X. Li, B. Liu, Z. Liu, F. Lu, F. Lu, G. Lu, C. Luo, X. Wang, Z. Wang, C. Ye and X. Yu for help with genotyping and sample collection; X. Feng, Y. Li, J. Ren and X. Zhou for help with sample collection; J. Fan, W. Gu, W. Guan, S. Hu, H. Jiang, R. Lei, Y. Lin, Z. Niu, B. Wang, L. Yang, W. Yang, Y. Wang, Z. Wang, S. Xu, W. Yan, H. Yang, W. Yuan, C. Zhang, J. Zhang, K. Zhang and G. Zhao for help with genotyping; P. Fong, C. Lai, C. Lau, T. Leung, L. Luk and W. Tong for help with genotyping; C. Pang for help with genotyping; K. Ding, B. Qiang, J. Zhang, X. Zhang and K. Zhou for help with genotyping; Q. Fu, S. Ghose, X. Lu, D. Nelson, A. Perez, S. Poole, R. Vega and H. Yonath for help with genotyping; C. Bruckner, T. Brundage, S. Chow, O. Iartchouk, M. Jain, M. Moorhead and K. Tran for help with genotyping; N. Addleman, J. Atilano, T. Chan, C. Chu, C. Ha, T. Nguyen, M. Minton and A. Phong for help with genotyping, and D. Lind for help with quality control and experimental design; R. Donaldson and S. Duan for help with genotyping, and J. Rice and N. Saccone for help with experimental design; J. Wigginton for help with implementing and testing QA/QC software; A. Clark, B. Keats, R. Myers, D. Nickerson and A. Williamson for providing advice to NIH; C. Juenger, C. Bennet, C. Bird, J. Melone, P. Nailer, M. Weiss, J. Witonsky and E. DeHaut-Combs for help with project management; M. Gray for organizing phone calls and meetings; D. Leja for help with figures; the Yoruba people of Ibadan, Nigeria, the people of Tokyo, Japan, and the community at Beijing Normal University, who participated in public consultations and community engagements; the people in these communities who donated their blood samples; and the people in the Utah CEPH community who allowed the samples they donated earlier to be used for the Project. This work was supported by the Japanese Ministry of Education, Culture, Sports, Science and Technology, the Wellcome Trust, Nuffield Trust, Wolfson Foundation, UK EPSRC, Genome Canada, Génome Québec, the Chinese Academy of Sciences, the Ministry of Science and Technology of the People’s Republic of China, the National Natural Science Foundation of China, the Hong Kong Innovation and Technology Commission, the University Grants Committee of Hong Kong, the SNP Consortium, the US National Institutes of Health (FIC, NCI, NCRR, NEI, NHGRI, NIA, NIAAA, NIAID, NIAMS, NIBIB, NIDA, NIDCD, NIDCR, NIDDK, NIEHS, NIGMS, NIMH, NINDS, NLM, OD), the W.M. Keck Foundation, and the Delores Dore Eccles Foundation. All SNPs genotyped within the HapMap Project are available from dbSNP (http://www.ncbi.nlm.nih.gov/SNP); all genotype information is available from dbSNP and the HapMap website (http://www.hapmap.org).

Author information

Authors and Affiliations

  1. The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA.,

    Kelly A. Frazer (Principal Investigator) & Sarah S. Murray

  2. Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, California 94043, USA.,

    Dennis G. Ballinger, David R. Cox, David A. Hinds & Laura L. Stuve

  3. Department of Molecular and Human Genetics, Baylor College of Medicine, Human Genome Sequencing Center, 1 Baylor Plaza, Houston, Texas 77030, USA.,

    Richard A. Gibbs (Principal Investigator), John W. Belmont, Suzanne M. Leal, David A. Wheeler, Richard A. Gibbs (Principal Investigator), John W. Belmont, Donna Muzny, Lynne Nazareth, Erica Sodergren, George M. Weinstock, David A. Wheeler & Imtaz Yakub

  4. Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA.,

    Andrew Boudreau, Thomas D. Willis & Jean-François Olivier

  5. Pacific Biosciences, 1505 Adams Drive, Menlo Park, California 94025, USA.,

    Paul Hardenbol

  6. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.,

    Shiran Pasternak, Lalitha Krishnan, Albert Vernon Smith & Marcela K. Tello-Ruiz

  7. The Broad Institute of Harvard and Massachusetts Institute of Technology, 1 Kendall Square, Cambridge, Massachusetts 02139, USA.,

    Fuli Yu, Stacey B. Gabriel (Project Leader), Rachel Barry, Brendan Blumenstiel, Amy Camargo, Matthew Defelice, Maura Faggart, Mary Goyette, Supriya Gupta, Jamie Moore, Huy Nguyen, Robert C. Onofrio, Melissa Parkin, Jessica Roy, Erich Stahl, Ellen Winchester, Liuda Ziaugra, David Altshuler (Principal Investigator), Mark J. Daly (Project Leader), Paul I. W. de Bakker, Jeff Barrett, Yves R. Chretien, Julian Maller, Steve McCarroll, Nick Patterson, Alkes Price, Daniel J. Richter, Pardis Sabeti, Richa Saxena, Stephen F. Schaffner, Patrick Varilly, David Altshuler (Principal Investigator), Lincoln D. Stein (Principal Investigator), Chris Spencer, Stacey B. Gabriel (Project Leader), Robert C. Onofrio, Daniel J. Richter, Liuda Ziaugra, Bruce W. Birren, Mark J. Daly & David Altshuler (Principal Investigator)

  8. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 100300, China.,

    Huanming Yang (Principal Investigator), Changqing Zeng (Principal Investigator), Yang Gao, Haoran Hu, Weitao Hu, Chaohua Li, Wei Lin, Siqi Liu, Hao Pan, Xiaoli Tang, Jian Wang, Wei Wang, Jun Yu, Bo Zhang, Qingrun Zhang, Hongbin Zhao, Hui Zhao, Jun Zhou, Changqing Zeng & Hui Zhao

  9. Massachusetts General Hospital and Harvard Medical School, Simches Research Center, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,

    David Altshuler (Principal Investigator), Mark J. Daly (Project Leader), Paul I. W. de Bakker, Jeff Barrett, Julian Maller, Steve McCarroll, Shaun Purcell, Richa Saxena, David Altshuler (Principal Investigator), Lincoln D. Stein (Principal Investigator), Mark J. Daly & David Altshuler (Principal Investigator)

  10. Chinese National Human Genome Center at Beijing, 3-707 N. Yongchang Road, Beijing Economic-Technological Development Area, Beijing 100176, China.,

    Yan Shen (Principal Investigator) & Zhijian Yao

  11. Chinese National Human Genome Center at Shanghai, 250 Bi Bo Road, Shanghai 201203, China.,

    Wei Huang (Principal Investigator), Xun Chu, Yungang He, Yangfan Liu, Yayun Shen, Weiwei Sun, Haifeng Wang, Yi Wang, Ying Wang, Xiaoyan Xiong & Liang Xu

  12. Fudan University and CAS-MPG Partner Institute for Computational Biology, School of Life Sciences, SIBS, CAS, Shanghai 201203, China.,

    Li Jin

  13. Department of Biochemistry, The Chinese University of Hong Kong, The Croucher Laboratory for Human Genetics, 6/F Mong Man Wai Building, Shatin, Hong Kong.,

    Mary M. Y. Waye (Principal Investigator) & Stephen K. W. Tsui

  14. Department of Biochemistry and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Knowloon, Hong Kong.,

    Hong Xue (Principal Investigator) & J. Tze-Fei Wong

  15. Illumina, 9885 Towne Centre Drive, San Diego, California 92121, USA.,

    Luana M. Galver (Principal Investigator), Jian-Bing Fan, Kevin Gunderson, Stéphanie Roumy & Arthur L. Holden

  16. Complete Genomics, Inc., 658 North Pastoria Avenue, Sunnyvale, California 94085, USA.,

    Arnold R. Oliphant

  17. Prognosys Biosciences, Inc., 4215 Sorrento Valley Boulevard, Suite 105, San Diego, California 92121, USA.,

    Mark S. Chee

  18. McGill University and Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Montréal, Québec H3A 1A4, Canada.,

    Alexandre Montpetit (Principal Investigator), Fanny Chagnon, Vincent Ferretti, Martin Leboeuf, Michael S. Phillips & Andrei Verner

  19. University of Montréal, The Public Law Research Centre (CRDP), PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada.,

    Clémentine Sallée & Bartha M. Knoppers

  20. Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 500, Toronto, Ontario M5G 1L7, Canada.,

    Thomas J. Hudson (Principal Investigator)

  21. University of California, San Francisco, Cardiovascular Research Institute, 513 Parnassus Avenue, Box 0793, San Francisco, California 94143, USA.,

    Pui-Yan Kwok (Principal Investigator), Dongmei Cai, Ludmila Pawlikowska & Ming Xiao

  22. Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, Box 8232, St Louis, Missouri 63110, USA.,

    Daniel C. Koboldt, Raymond D. Miller & Patricia Taillon-Miller

  23. University of Hong Kong, Genome Research Centre, 6/F, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong.,

    Lap-Chee Tsui (Principal Investigator), William Mak, You Qiang Song, Paul K. H. Tam & Pak C. Sham

  24. University of Tokyo, Institute of Medical Science, 4-6-1 Sirokanedai, Minato-ku, Tokyo 108-8639, Japan.,

    Yusuke Nakamura (Principal Investigator)

  25. RIKEN SNP Research Center, 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan.,

    Yusuke Nakamura (Principal Investigator), Takahisa Kawaguchi, Takuya Kitamoto, Takashi Morizono, Atsushi Nagashima, Yozo Ohnishi, Akihiro Sekine, Toshihiro Tanaka, Tatsuhiko Tsunoda, Tatsuhiko Tsunoda (Principal Investigator) & Todd Johnson

  26. Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,

    Panos Deloukas (Project Leader), Christine P. Bird, Marcos Delgado, Emmanouil T. Dermitzakis, Rhian Gwilliam, Sarah Hunt, Don Powell, Barbara E. Stranger, Pamela Whittaker, Jane Rogers (Principal Investigator), John Burton, Nigel P. Carter, Christopher M. Clee, Mark Griffiths, Matthew C. Jones, Kirsten McLay, Robert W. Plumb, Mark T. Ross, Sarah K. Sims & David L. Willey

  27. Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK.,

    Jonathan Morrison

  28. Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK.,

    David R. Bentley (Principal Investigator)

  29. Columbia University, 500 West 120th Street, New York, New York 10027, USA.,

    Itsik Pe’er

  30. Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.,

    Gudmundur A. Thorisson

  31. Johns Hopkins University School of Medicine, McKusick-Nathans Institute of Genetic Medicine, Broadway Research Building, Suite 579, 733 North Broadway, Baltimore, Maryland 21205, USA.,

    Aravinda Chakravarti (Principal Investigator), Peter E. Chen, David J. Cutler, Carl S. Kashuk & Shin Lin

  32. Department of Biostatistics, University of Michigan, Center for Statistical Genetics, 1420 Washington Heights, Ann Arbor, Michigan 48109, USA.,

    Gonçalo R. Abecasis (Principal Investigator), Weihua Guan, Yun Li & Zhaohui Steve Qin

  33. International Epidemiology Institute, 1455 Research Boulevard, Suite 550, Rockville, Maryland 20850, USA.,

    Heather M. Munro

  34. Center for Biomolecular Science and Engineering, Engineering 2, Suite 501, Mail Stop CBSE/ITI, UC Santa Cruz, Santa Cruz, California 95064, USA.,

    Daryl J. Thomas

  35. Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.,

    Gilean McVean (Project Leader), Adam Auton, Leonardo Bottolo, Niall Cardin, Susana Eyheramendy, Colin Freeman, Jonathan Marchini, Simon Myers & Peter Donnelly (Principal Investigator)

  36. Department of Statistics, University of Chicago, 5734 South University Avenue, Eckhart Hall, Room 126, Chicago, Illinois 60637, USA.,

    Matthew Stephens

  37. Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.,

    Lon R. Cardon (Principal Investigator)

  38. University of Oxford/Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.,

    Geraldine Clarke, David M. Evans & Andrew P. Morris

  39. University of Washington Department of Biostatistics, Box 357232, Seattle, Washington 98195, USA.,

    Bruce S. Weir

  40. US National Institutes of Health, National Human Genome Research Institute, 50 South Drive, Bethesda, Maryland 20892, USA.,

    James C Mullikin

  41. US National Institutes of Health, National Library of Medicine, National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, USA.,

    Stephen T. Sherry & Michael Feolo

  42. Department of Medicine, University of Chicago, Section of Genetic Medicine, 5801 South Ellis, Chicago, Illinois 60637, USA.,

    Andrew Skol

  43. Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China.,

    Houcan Zhang

  44. Health Sciences University of Hokkaido, Ishikari Tobetsu Machi 1757, Hokkaido 061-0293, Japan.,

    Ichiro Matsuda (Principal Investigator)

  45. Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Japan.,

    Yoshimitsu Fukushima

  46. United Nations Educational, Scientific and Cultural Organization (UNESCO Bangkok), 920 Sukhumwit Road, Prakanong, Bangkok 10110, Thailand.,

    Darryl R. Macer

  47. University of Tsukuba, Eubios Ethics Institute, PO Box 125, Tsukuba Science City 305-8691, Japan.,

    Eiko Suda

  48. Howard University, National Human Genome Center, 2216 6th Street, NW, Washington DC 20059, USA.,

    Charles N. Rotimi (Principal Investigator) & Charmaine D. M. Royal

  49. University of Ibadan College of Medicine, Ibadan, Oyo State, Nigeria.,

    Clement A. Adebamowo, Ike Ajayi, Toyin Aniagwu, Chibuzor Nkwodimmah & Isaac F. Adewole

  50. Department of Bioethics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.,

    Patricia A. Marshall

  51. Department of Human Genetics, University of Utah, Eccles Institute of Human Genetics, 15 North 2030 East, Salt Lake City, Utah 84112, USA.,

    Mark F. Leppert (Principal Investigator), Missy Dixon & Andy Peiffer

  52. Chinese Academy of Social Sciences, Institute of Philosophy/Center for Applied Ethics, 2121, Building 9, Caoqiao Xinyuan 3 Qu, Beijing 100067, China.,

    Renzong Qiu

  53. Genetic Interest Group, 4D Leroy House, 436 Essex Road, London N130P, UK.,

    Alastair Kent

  54. Kyoto University, Institute for Research in Humanities and Graduate School of Biostudies, Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.,

    Kazuto Kato

  55. Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Sakamoto 1-12-4, Nagasaki 852-8523, Japan.,

    Norio Niikawa

  56. Department of Anthropology, University of Oklahoma, 455 West Lindsey Street, Norman, Oklahoma 73019, USA.,

    Morris W. Foster

  57. Vanderbilt University, Center for Genetics and Health Policy, 507 Light Hall, Nashville, Tennessee 37232, USA.,

    Ellen Wright Clayton

  58. Wellcome Trust, 215 Euston Road, London NW1 2BE, UK.,

    Jessica Watkin, Ruth Jamieson & John Stewart

  59. Washington University School of Medicine, Genome Sequencing Center, Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.,

    Richard K. Wilson & Lucinda L. Fulton

  60. Chinese Academy of Sciences, 52 Sanlihe Road, Beijing 100864, China.,

    Zhu Chen, Hua Han & Le Kang

  61. Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, Ontario K2P 1P1, Canada.,

    Martin Godbout & Karen Kennedy

  62. McGill University, Office of Technology Transfer, 3550 University Street, Montréal, Québec H3A 2A7, Canada.,

    John C. Wallenburg

  63. Génome Québec, 630, boulevard René-Lévesque Ouest, Montréal, Québec H3B 1S6, Canada.,

    Paul L’Archevêque & Guy Bellemare

  64. Ministry of Education, Culture, Sports, Science, and Technology, 3-2-2 Kasumigaseki, Chiyodaku, Tokyo 100-8959, Japan.,

    Koji Saeki

  65. Ministry of Science and Technology of the People’s Republic of China, 15 B. Fuxing Road, Beijing 100862, China.,

    Hongguang Wang, Daochang An, Hongbo Fu, Qing Li & Zhen Wang

  66. The Human Genetic Resource Administration of China, b7, Zaojunmiao, Haidian District, Beijing 100081, China.,

    Renwu Wang

  67. US National Institutes of Health, National Human Genome Research Institute, 5635 Fishers Lane, Bethesda, Maryland 20892, USA.,

    Lisa D. Brooks, Jean E. McEwen, Mark S. Guyer, Vivian Ota Wang, Jane L. Peterson & Lynn F. Zacharia

  68. US National Institutes of Health, Office of Behavioral and Social Science Research, 31 Center Drive, Bethesda, Maryland 20892, USA.,

    Vivian Ota Wang

  69. Novartis Pharmaceuticals Corporation, Biomarker Development, One Health Plaza, East Hanover, New Jersey 07936, USA.,

    Michael Shi

  70. US National Institutes of Health, Office of Technology Transfer, 6011 Executive Boulevard, Rockville, Maryland 20852, USA.,

    Jack Spiegel

  71. University of Maryland School of Law, 500 West Baltimore Street, Baltimore, Maryland 21201, USA.,

    Lawrence M. Sung

  72. US National Institutes of Health, National Human Genome Research Institute, 31 Center Drive, Bethesda, Maryland 20892, USA.,

    Francis S. Collins

Consortia

The International HapMap Consortium

  • Genotyping centres: Perlegen Sciences

    • Kelly A. Frazer (Principal Investigator)
    • , Dennis G. Ballinger
    • , David R. Cox
    • , David A. Hinds
    •  & Laura L. Stuve

  • Baylor College of Medicine and ParAllele BioScience

    • Richard A. Gibbs (Principal Investigator)
    • , John W. Belmont
    • , Andrew Boudreau
    • , Paul Hardenbol
    • , Suzanne M. Leal
    • , Shiran Pasternak
    • , David A. Wheeler
    • , Thomas D. Willis
    •  & Fuli Yu

  • Beijing Genomics Institute

    • Huanming Yang (Principal Investigator)
    • , Changqing Zeng (Principal Investigator)
    • , Yang Gao
    • , Haoran Hu
    • , Weitao Hu
    • , Chaohua Li
    • , Wei Lin
    • , Siqi Liu
    • , Hao Pan
    • , Xiaoli Tang
    • , Jian Wang
    • , Wei Wang
    • , Jun Yu
    • , Bo Zhang
    • , Qingrun Zhang
    • , Hongbin Zhao
    • , Hui Zhao
    •  & Jun Zhou

  • Broad Institute of Harvard and Massachusetts Institute of Technology

    • Stacey B. Gabriel (Project Leader)
    • , Rachel Barry
    • , Brendan Blumenstiel
    • , Amy Camargo
    • , Matthew Defelice
    • , Maura Faggart
    • , Mary Goyette
    • , Supriya Gupta
    • , Jamie Moore
    • , Huy Nguyen
    • , Robert C. Onofrio
    • , Melissa Parkin
    • , Jessica Roy
    • , Erich Stahl
    • , Ellen Winchester
    • , Liuda Ziaugra
    •  & David Altshuler (Principal Investigator)

  • Chinese National Human Genome Center at Beijing

    • Yan Shen (Principal Investigator)
    •  & Zhijian Yao

  • Chinese National Human Genome Center at Shanghai

    • Wei Huang (Principal Investigator)
    • , Xun Chu
    • , Yungang He
    • , Li Jin
    • , Yangfan Liu
    • , Yayun Shen
    • , Weiwei Sun
    • , Haifeng Wang
    • , Yi Wang
    • , Ying Wang
    • , Xiaoyan Xiong
    •  & Liang Xu

  • Chinese University of Hong Kong

    • Mary M. Y. Waye (Principal Investigator)
    •  & Stephen K. W. Tsui

  • Hong Kong University of Science and Technology

    • Hong Xue (Principal Investigator)
    •  & J. Tze-Fei Wong

  • Illumina

    • Luana M. Galver (Principal Investigator)
    • , Jian-Bing Fan
    • , Kevin Gunderson
    • , Sarah S. Murray
    • , Arnold R. Oliphant
    •  & Mark S. Chee

  • McGill University and Génome Québec Innovation Centre

    • Alexandre Montpetit (Principal Investigator)
    • , Fanny Chagnon
    • , Vincent Ferretti
    • , Martin Leboeuf
    • , Jean-François Olivier
    • , Michael S. Phillips
    • , Stéphanie Roumy
    • , Clémentine Sallée
    • , Andrei Verner
    •  & Thomas J. Hudson (Principal Investigator)

  • University of California at San Francisco and Washington University

    • Pui-Yan Kwok (Principal Investigator)
    • , Dongmei Cai
    • , Daniel C. Koboldt
    • , Raymond D. Miller
    • , Ludmila Pawlikowska
    • , Patricia Taillon-Miller
    •  & Ming Xiao

  • University of Hong Kong

    • Lap-Chee Tsui (Principal Investigator)
    • , William Mak
    • , You Qiang Song
    •  & Paul K. H. Tam

  • University of Tokyo and RIKEN

    • Yusuke Nakamura (Principal Investigator)
    • , Takahisa Kawaguchi
    • , Takuya Kitamoto
    • , Takashi Morizono
    • , Atsushi Nagashima
    • , Yozo Ohnishi
    • , Akihiro Sekine
    • , Toshihiro Tanaka
    •  & Tatsuhiko Tsunoda

  • Wellcome Trust Sanger Institute

    • Panos Deloukas (Project Leader)
    • , Christine P. Bird
    • , Marcos Delgado
    • , Emmanouil T. Dermitzakis
    • , Rhian Gwilliam
    • , Sarah Hunt
    • , Jonathan Morrison
    • , Don Powell
    • , Barbara E. Stranger
    • , Pamela Whittaker
    •  & David R. Bentley (Principal Investigator)

  • Analysis groups: Broad Institute

    • Mark J. Daly (Project Leader)
    • , Paul I. W. de Bakker
    • , Jeff Barrett
    • , Yves R. Chretien
    • , Julian Maller
    • , Steve McCarroll
    • , Nick Patterson
    • , Itsik Pe’er
    • , Alkes Price
    • , Shaun Purcell
    • , Daniel J. Richter
    • , Pardis Sabeti
    • , Richa Saxena
    • , Stephen F. Schaffner
    • , Pak C. Sham
    • , Patrick Varilly
    •  & David Altshuler (Principal Investigator)

  • Cold Spring Harbor Laboratory

    • Lincoln D. Stein (Principal Investigator)
    • , Lalitha Krishnan
    • , Albert Vernon Smith
    • , Marcela K. Tello-Ruiz
    •  & Gudmundur A. Thorisson

  • Johns Hopkins University School of Medicine

    • Aravinda Chakravarti (Principal Investigator)
    • , Peter E. Chen
    • , David J. Cutler
    • , Carl S. Kashuk
    •  & Shin Lin

  • University of Michigan

    • Gonçalo R. Abecasis (Principal Investigator)
    • , Weihua Guan
    • , Yun Li
    • , Heather M. Munro
    • , Zhaohui Steve Qin
    •  & Daryl J. Thomas

  • University of Oxford

    • Gilean McVean (Project Leader)
    • , Adam Auton
    • , Leonardo Bottolo
    • , Niall Cardin
    • , Susana Eyheramendy
    • , Colin Freeman
    • , Jonathan Marchini
    • , Simon Myers
    • , Chris Spencer
    • , Matthew Stephens
    •  & Peter Donnelly (Principal Investigator)

  • University of Oxford,Wellcome Trust Centre for Human Genetics

    • Lon R. Cardon (Principal Investigator)
    • , Geraldine Clarke
    • , David M. Evans
    • , Andrew P. Morris
    •  & Bruce S. Weir

  • RIKEN

    • Tatsuhiko Tsunoda (Principal Investigator)
    •  & Todd Johnson

  • US National Institutes of Health

    • James C Mullikin

  • US National Institutes of Health National Center for Biotechnology Information

    • Stephen T. Sherry
    • , Michael Feolo
    •  & Andrew Skol

  • Community engagement/public consultation and sample collection groups: Beijing Normal University and Beijing Genomics Institute

    • Houcan Zhang
    • , Changqing Zeng
    •  & Hui Zhao

  • Health Sciences University of Hokkaido, Eubios Ethics Institute, and Shinshu University

    • Ichiro Matsuda (Principal Investigator)
    • , Yoshimitsu Fukushima
    • , Darryl R. Macer
    •  & Eiko Suda

  • Howard University and University of Ibadan

    • Charles N. Rotimi (Principal Investigator)
    • , Clement A. Adebamowo
    • , Ike Ajayi
    • , Toyin Aniagwu
    • , Patricia A. Marshall
    • , Chibuzor Nkwodimmah
    •  & Charmaine D. M. Royal

  • University of Utah

    • Mark F. Leppert (Principal Investigator)
    • , Missy Dixon
    •  & Andy Peiffer

  • Ethical, legal and social issues: Chinese Academy of Social Sciences

    • Renzong Qiu

  • Genetic Interest Group

    • Alastair Kent

  • Kyoto University

    • Kazuto Kato

  • Nagasaki University

    • Norio Niikawa

  • University of Ibadan School of Medicine

    • Isaac F. Adewole

  • University of Montréal

    • Bartha M. Knoppers

  • University of Oklahoma

    • Morris W. Foster

  • Vanderbilt University

    • Ellen Wright Clayton

  • Wellcome Trust

    • Jessica Watkin

  • SNP discovery: Baylor College of Medicine

    • Richard A. Gibbs (Principal Investigator)
    • , John W. Belmont
    • , Donna Muzny
    • , Lynne Nazareth
    • , Erica Sodergren
    • , George M. Weinstock
    • , David A. Wheeler
    •  & Imtaz Yakub

  • Broad Institute of Harvard and Massachusetts Institute of Technology

    • Stacey B. Gabriel (Project Leader)
    • , Robert C. Onofrio
    • , Daniel J. Richter
    • , Liuda Ziaugra
    • , Bruce W. Birren
    • , Mark J. Daly
    •  & David Altshuler (Principal Investigator)

  • Washington University

    • Richard K. Wilson
    •  & Lucinda L. Fulton

  • Wellcome Trust Sanger Institute

    • Jane Rogers (Principal Investigator)
    • , John Burton
    • , Nigel P. Carter
    • , Christopher M. Clee
    • , Mark Griffiths
    • , Matthew C. Jones
    • , Kirsten McLay
    • , Robert W. Plumb
    • , Mark T. Ross
    • , Sarah K. Sims
    •  & David L. Willey

  • Scientific management: Chinese Academy of Sciences

    • Zhu Chen
    • , Hua Han
    •  & Le Kang

  • Genome Canada

    • Martin Godbout
    •  & John C. Wallenburg

  • Génome Québec

    • Paul L’Archevêque
    •  & Guy Bellemare

  • Japanese Ministry of Education, Culture, Sports, Science and Technology

    • Koji Saeki

  • Ministry of Science and Technology of the People’s Republic of China

    • Hongguang Wang
    • , Daochang An
    • , Hongbo Fu
    • , Qing Li
    •  & Zhen Wang

  • The Human Genetic Resource Administration of China

    • Renwu Wang

  • The SNP Consortium

    • Arthur L. Holden

  • US National Institutes of Health

    • Lisa D. Brooks
    • , Jean E. McEwen
    • , Mark S. Guyer
    • , Vivian Ota Wang
    • , Jane L. Peterson
    • , Michael Shi
    • , Jack Spiegel
    • , Lawrence M. Sung
    • , Lynn F. Zacharia
    •  & Francis S. Collins

  • Wellcome Trust

    • Karen Kennedy
    • , Ruth Jamieson
    •  & John Stewart

Corresponding authors

Correspondence to Mark J. Daly (Project Leader) or Gilean McVean (Project Leader).

Ethics declarations

Competing interests

Some authors declare employment and personal financial interests. These authors declare employment financial interests: authors who are current employees of genotyping companies or were employees of genotyping companies (Affymetrix, Illumina, ParAllele, Perlegen) during the project. These authors declare personal financial interests (defined as serving on the advisory board of a genotyping company, owning stock in a genotyping company, or receiving royalties from a patent licensed to a genotyping company): A.B., A.C., A.S., D.R.C., M.S.C., J.B.F., L.M.G., L.R.C., P.H., P.Y.K., S.S.M. and T.D.W.

Additional information

Lists of participants and affiliations appear at the end of the paper. (Participants are arranged by institution and then alphabetically within institutions except for Principal Investigators and Project Leaders, as indicated.)

Supplementary information

Supplementary Information

The file contains Supplementary Notes, Supplementary Tables 1-9, Supplementary Figures 1-7 with Legends and additional references. (PDF 4470 kb)

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The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007). https://doi.org/10.1038/nature06258

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  • DOI: https://doi.org/10.1038/nature06258

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