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Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability

Nature Geneticsvolume 50pages652656 (2018) | Download Citation


Hair color is one of the most recognizable visual traits in European populations and is under strong genetic control. Here we report the results of a genome-wide association study meta-analysis of almost 300,000 participants of European descent. We identified 123 autosomal and one X-chromosome loci significantly associated with hair color; all but 13 are novel. Collectively, single-nucleotide polymorphisms associated with hair color within these loci explain 34.6% of red hair, 24.8% of blond hair, and 26.1% of black hair heritability in the study populations. These results confirm the polygenic nature of complex phenotypes and improve our understanding of melanin pigment metabolism in humans.

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This research has been conducted using the UK Biobank Resource under Application Number 12052.

The ALSPAC work is supported by a Medical Research Council program grant (MC_UU_12013/4 to D.M.E). The UK Medical Research Council and the Wellcome Trust (grant refs: 092731 and 102215/2/13/2) and the University of Bristol provide core support for ALSPAC. D.M.E. is supported by an Australian Research Council Future Fellowship (FT130101709). This publication is the work of the authors and D.M.E. will serve as guarantor for the contents of this paper. ALSPAC GWAS data was generated by Sample Logistics and Genotyping Facilities at the Wellcome Trust Sanger Institute and LabCorp (Laboratory Corporation of America) using support from 23andMe.

The ERF Study was supported by the joint grant from the Netherlands Organization for Scientific Research (NWO, 91203014), the Center of Medical Systems Biology (CMSB), Hersenstichting Nederland, Internationale Stichting Alzheimer Onderzoek (ISAO), Alzheimer Association project number 04516, Hersenstichting Nederland project number 12F04(2).76, and the Interuniversity Attraction Poles (IUAP) program. As a part of EUROSPAN (European Special Populations Research Network), ERF was supported by European Commission FP6 STRP grant number 018947 (LSHG-CT-2006-01947) and also received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)/grant agreement HEALTH-F4-2007-201413 by the European Commission under the program “Quality of Life and Management of the Living Resources” of 5th Framework Programme (no. QLG2-CT-2002-01254). High-throughput analysis of the ERF data was supported by joint grant from Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043).

The INGI research was supported by funds from Compagnia di San Paolo, Torino, Italy; Fondazione Cariplo, Italy and Ministry of Health, Ricerca Finalizzata 2008 and CCM 2010 and Telethon, Italy. Additional support was provided by the Italian Ministry of Health (RF 2010 to PG), FVG Region, and Fondo Trieste.

The NTR study was supported by multiple grants from the Netherlands Organization for Scientific Research (NWO: 016-115-035, 463-06-001, 451-04-034), ZonMW (31160008, 911-09-032); from the Institute for Health and Care Research (EMGO + ); and from the Biomolecular Resources Research Infrastructure (BBMRI-NL, 184.021.007), European Research Council (ERC-230374). Genotyping was made possible by grants from NWO/SPI 56-464-14192, Genetic Association Information Network (GAIN) of the Foundation for the National Institutes of Health, Rutgers University Cell and DNA Repository (NIMH U24 MH068457-06), the Avera Institute, Sioux Falls (USA), and the National Institutes of Health (NIH R01 HD042157-01A1, MH081802, Grand Opportunity grants 1RC2 MH089951 and 1RC2 MH089995). B.D.L. is supported by a PhD grant (201206180099) from the China Scholarship Council.

QIMR funding was provided by the Australian National Health and Medical Research Council (241944, 339462, 389927, 389875, 389891, 389892, 389938, 442915, 442981, 496739, 552485, 552498), the Australian Research Council (A7960034, A79906588, A79801419, DP0770096, DP0212016, DP0343921), the FP-5 GenomEUtwin Project (QLG2-CT-2002-01254), and the US National Institutes of Health (NIH grants AA07535, AA10248, AA13320, AA13321, AA13326, AA14041, MH66206). Statistical analyses were carried out on the Genetic Cluster Computer, which is financially supported by the Netherlands Scientific Organization (NWO 480-05-003). S.E.M. and D.L.D. are supported by the National Health and Medical Research Council (NHMRC) Fellowship Scheme.

The 20-year follow-up of Generation 2 of the Western Australian Pregnancy Cohort (Raine) Study was funded by Australian National Health and Medical Research Council (NHMRC) project grant 1021105, Lions Eye Institute, the Australian Foundation for the Prevention of Blindness, and the Ophthalmic Research Institute of Australia. S.Y. is supported by NHMRC Early Career Fellowship (CJ Martin - Overseas Biomedical Fellowship).

The Rotterdam Study is supported by the Netherlands Organization of Scientific Research NWO Investments (nr. 175.010.2005.011, 911-03-012). This study is funded by the Research Institute for Diseases in the Elderly (014-93-015; RIDE2), the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) project nr. 050-060-810. The Rotterdam Study is supported by the Erasmus MC and Erasmus University Rotterdam; the Netherlands Organization for Scientific Research (NWO); the Netherlands Organization for Health Research and Development (ZonMw); the Research Institute for Diseases in the Elderly (RIDE) the Netherlands Genomics Initiative (NGI); the Ministry of Education, Culture and Science; the Ministry of Health Welfare and Sport; the European Commission (DG XII); and the Municipality of Rotterdam. The generation and management of GWAS genotype data for the Rotterdam Study were executed by the Human Genotyping Facility of the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC. F.L. is supported by a Chinese recruiting program, the National Thousand Young Talents Award, and by the National Natural Science Foundation of China (NSFC) (91651507).

The TwinsUK study was funded by the Wellcome Trust (105022/Z/14/Z); European Community's Seventh Framework Programme (FP7/2007-2013). The study also receives support from the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas’ NHS Foundation Trust in partnership with King's College London. SNP genotyping was performed by the Wellcome Trust Sanger Institute and National Eye Institute via NIH/CIDR.

Author information

Author notes

  1. A list of members and affiliations appears in the Supplementary Note.

  2. These authors contributed equally: Pirro G. Hysi, Ana Valdes, Fan Liu.

  3. These authors jointly supervised this work: Manfred Kayser, Timothy D. Spector.


  1. King’s College London Department of Twins Research and Genetic Epidemiology, London, UK

    • Pirro G. Hysi
    • , Ana M. Valdes
    • , Veronique Bataille
    • , Alessia Visconti
    • , Mario Falchi
    •  & Timothy D. Spector
  2. Department of Ophthalmology, King’s College London, London, UK

    • Pirro G. Hysi
  3. Division of Rheumatology, Orthopaedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, UK

    • Ana M. Valdes
  4. Nottingham NIHR Biomedical Research Centre, Nottingham, United Kingdom

    • Ana M. Valdes
  5. CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China

    • Fan Liu
    • , Yan Chen
    •  & Changqing Zeng
  6. University of Chinese Academy of Sciences, Beijing, PR China

    • Fan Liu
    •  & Yan Chen
  7. Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands

    • Fan Liu
    •  & Manfred Kayser
  8. 23andMe, Inc., Mountain View, CA, USA

    • Nicholas A. Furlotte
    •  & David A. Hinds
  9. University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, Australia

    • David M. Evans
  10. MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK

    • David M. Evans
    • , Gibran Hemani
    • , George McMahon
    • , Susan M. Ring
    •  & George Davey Smith
  11. QIMR Berghofer Medical Research Institute, Brisbane, Australia

    • David L. Duffy
    • , Gu Zhu
    • , Scott D. Gordon
    • , Sarah E. Medland
    •  & Nicholas G. Martin
  12. Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands

    • Bochao D. Lin
    • , Gonneke Willemsen
    • , Jouke Jan Hottenga
    •  & Dorret I. Boomsma
  13. Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy

    • Dragana Vuckovic
    • , Giorgia Girotto
    • , Ilaria Gandin
    • , Cinzia Sala
    • , Marco Brumat
    •  & Paolo Gasparini
  14. Institute for Maternal and Child Health IRCCS “Burlo Garofolo”, Trieste, Italy

    • Giorgia Girotto
    • , Maria Pina Concas
    • , Paolo Gasparini
    • , Massimiliano Cocca
    •  & Antonietta Robino
  15. Division of Genetics and Cell Biology, San Faffaele Research Institute, Milano, Italy

    • Daniela Toniolo
  16. Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, WA, Australia

    • Seyhan Yazar
    • , Alex W. Hewitt
    •  & David A. Mackey
  17. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK

    • Seyhan Yazar
  18. Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Australia

    • Alex W. Hewitt
    •  & David A. Mackey
  19. School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia

    • Alex W. Hewitt
    •  & David A. Mackey
  20. Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands

    • Andre G. Uitterlinden
  21. Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands

    • Andre G. Uitterlinden
    • , M. Arfan Ikram
    •  & Cornelia M. van Duijn
  22. Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands

    • Merel A. Hamer
    •  & Tamar Nijsten


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  1. The International Visible Trait Genetics Consortium

    1. The International Visible Trait Genetics Consortium


      P.G.H., A. Valdes, and F.L. jointly wrote the manuscript, coordinated meta-analyses, and performed prediction modeling. N.A.F., D.M.E., V.B., A. Visconti, G.H., G.M., S.M.R., D.L.D., G.Z., S.D.G., S.E.M., B.D.L., G.W., J.J.H., D.V., G.G., I.G., C.S., M.P.C., M.B., D.T., M.C., A.R., S.Y., A.W.H., Y.C., C.Z., A.G.U., M.A.H., T.N., M.F., and D.A.H. each conducted part of the analyses described in this work. G.D.S., P.G., C.M.v.D., M.A.I., D.A.M., D.I.B., N.G.M., and M.F. contributed populations samples and data used for analyses. M.K. and T.D.S. jointly coordinated the work and participated in manuscript preparation.

      Competing interests

      N.A.F. and D.A.H. are employees of the 23andMe Inc., a consumer genetics company.

      Corresponding authors

      Correspondence to Manfred Kayser or Timothy D. Spector.

      Integrated supplementary information

      1. Supplementary Figure 1 Distribution of self-reported hair color in the UK Biobank and 23andMe cohorts.

        Plots show the densities for each hair color category in the UK Biobank (top) and 23andMe cohorts (bottom).

      2. Supplementary Figure 2 Plot of the first five principal components in UK Biobank and 23andMe subjects included in the analyses.

        The top-left panel shows the participants of European descent that were included in the analyses (blue) in the backdrop of all multi-ethnic UK Biobank and 23andMe participants. The plots for any two of the first principal components for the subjects of European descent (included in the analyses) are also given.

      3. Supplementary Figure 3 Violin plots of the first principal components for the UK Biobank and 23andMe participants.

        Each violin plot shows the distribution of principal components computed in the UK Biobank subjects (top) and the 23andMe cohort (bottom).

      4. Supplementary Figure 4 Expected variation of genomic control inflation factor (λ) as a function of sample size.

        The expected λ were calculated using the same number of loci, LD structure and trait heritability observed in the 23andMe cohort (blue) and the UK Biobank cohort (red) in absence of factors artificially inflating association. These genomic inflation factors observed in the discovery cohort are a reflection of the power of these large sample analyzed in presence of polygenicity; they would be merely the equivalent of a λGC = 1.0186 for the 23andMe cohort and λGC = 1.0221 for the UKBB cohort had the effective sample sizes been smaller (n = 20,000) and the underlying genetic effects remained the same.

      5. Supplementary Figure 5 Power to detect genome-wide significant associations.

        Plot generated using a sample of n = 140,000 subjects at α = 10-7. Power is shown for the most representative range of allele frequencies detected in GWAS (MAF = 0.10, red line; MAF = 0.30, blue line). The value on the y-axis denotes the probability that a true association would be detected at the pre-defined α; for example, for a locus with a MAF = 0.10 with an effect size of 0.035 s.d. per each copy of the risk allele over the trait, there is a 60% probability to replicate the same association at a genome-wide level of significance.

      6. Supplementary Figure 6 Correlation of effect sizes between men and women participating in the UK Biobank and the 23andMe cohorts.

        The black line denotes parity of effects, and each point represents one of the GWAS associated SNPs shown in Supplementary Table 2.

      7. Supplementary Figure 7 Evidence of natural selection for the SNPs significantly associated with hair color.

        Three different natural selection tests were selected (see Online Methods), and the values plotted here represent the centile rank of the natural selection score within European populations (iHS test, red), compared to YRI Africans (XP-EHH CEU vs. YRI, green) and to CHB Chinese populations (blue) using 1000 Genomes data. The plot shows an enrichment for higher ranks (lower centiles) of selection for some SNPs within European populations (two tailed Wilcoxon test P = 0.04), evidence for stronger selection for these SNPs in Europeans compared to Africans (two-tailed Wilcoxon P = 0.014), but less significant compared to Chinese (two tailed Wilcoxon P = 0.056).

      8. Supplementary Figure 8 Hair color prediction in participants of the Rotterdam and QIMR studies.

        The prediction model is based on multinomial logistic regression including 20 HIrisPlex SNPs, a polygenic score for blond-brown-black (233 SNPs), and a polygenic score for red (25 SNPs); see Supplementary Note for marker and model specifications.

      9. Supplementary Figure 9 Sex-specific prevalence of hair color categories in the UK Biobank and 23andMe cohorts.

        In both cohorts, there is a higher prevalence of blond, red and light brown hair colors among women and a higher prevalence of black and dark brown hair colors among men.

      Supplementary information

      1. Supplementary Figures

        Supplementary Figures 1–9

      2. Reporting Summary

      3. Supplementary Note and Supplementary Tables

        Supplementary Note 1 and Supplementary Tables 1–10

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