Genetics of skin color variation in Europeans: genome-wide association studies with functional follow-up
Open accessAbstract
In the International Visible Trait Genetics (VisiGen) Consortium, we investigated the genetics of human skin color by combining a series of genome-wide association studies (GWAS) in a total of 17,262 Europeans with functional follow-up of discovered loci. Our GWAS provide the first genome-wide significant evidence for chromosome 20q11.22 harboring the ASIP gene being explicitly associated with skin color in Europeans. In addition, genomic loci at 5p13.2 (SLC45A2), 6p25.3 (IRF4), 15q13.1 (HERC2/OCA2), and 16q24.3 (MC1R) were confirmed to be involved in skin coloration in Europeans. In follow-up gene expression and regulation studies of 22 genes in 20q11.22, we highlighted two novel genes EIF2S2 and GSS, serving as competing functional candidates in this region and providing future research lines. A genetically inferred skin color score obtained from the 9 top-associated SNPs from 9 genes in 940 worldwide samples (HGDP-CEPH) showed a clear gradual pattern in Western Eurasians similar to the distribution of physical skin color, suggesting the used 9 SNPs as suitable markers for DNA prediction of skin color in Europeans and neighboring populations, relevant in future forensic and anthropological investigations.
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In European populations, predictive models based on only 9 SNPs capture up to 16% of the variance in skin pigmentation.
“In European populations, predictive models based on only 9 SNPs capture up to 16% of the variance in skin pigmentation (Liu et al., 2015), highlighting its relative simplicity.”
From An Unexpectedly Complex Architecture for Skin Pigmentation in Africans (2017) · cites this paper as Liu et al., 2015
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- Authors
- Liu, F., Visser, M., Duffy, D. L., Hysi, P. G., Jacobs, L. C., Lao, O., Zhong, K., Walsh, S., Chaitanya, L., Wollstein, A., Zhu, G., Montgomery, G. W., Henders, A. K., Mangino, M., Glass, D., Bataille, V., Sturm, R. A., Rivadeneira, F., Hofman, A., van IJcken, W. F. J., Uitterlinden, A. G., Palstra, R.-J. T. S., Spector, T. D., Martin, N. G., Nijsten, T. E. C., & Kayser, M.
- Affiliations
- Erasmus MC (NL)
- QIMR Berghofer Medical Research Institute (AU)
- King's College London (GB)
- Translational Research Institute (AU)
- Corresponding author
- Liu, Fan
- Kayser, Manfred
- ORCID
- Liu, Fan
- Visser, Mijke
- Duffy, David L.
- Hysi, Pirro G.
- Jacobs, Leonie C.
- Zhong, Kaiyin
- Walsh, Susan
- Chaitanya, Lakshmi
- Zhu, Gu
- Montgomery, Grant W.
- Henders, Anjali K.
- Mangino, Massimo
- Glass, Daniel
- Bataille, Veronique
- Sturm, Richard A.
- Rivadeneira, Fernando
- Uitterlinden, André G.
- Palstra, Robert-Jan T. S.
- Martin, Nicholas G.
- Nijsten, Tamar E. C.
- Kayser, Manfred
- Venue
- Human Genetics
- Published
- 2015-05-12
- Volume
- 134
- Issue
- 8
- Pages
- 823-835
- ISSN
- 0018-7348 (ISSN-L)
- 0340-6717
- 1432-1203
- PMC
- PMC4495261
- OpenAlex
- W1750145230
- Cited by
- 172
- References
- 54
- Citations by year
- 2026: 9 · 2025: 10 · 2024: 15 · 2023: 12 · 2022: 16 · 2021: 18 · 2020: 21 · 2019: 18 · 2018: 17 · 2017: 22 · 2016: 10 · 2015: 4
- FWCI
- 9.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Human Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion, cc-by)
- RePub (Erasmus University Rotterdam) (submittedVersion)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by-nc-nd)
- PMC
- Funders
- Wellcome Trust
- National Institute for Health and Care Research (NF-SI-0514-10027)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (911-03-012, 175.010.200)
- Medical Research Council (MR/N01104X/1)
- Biotechnology and Biological Sciences Research Council (G20234)
- National Eye Institute (R01EY018246)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD050735, HD50735)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- skin color, pigmentation genetics, ASIP, SLC45A2, IRF4, MC1R, gene expression regulation, General Social Survey, forensic anthropology, European populations
- MeSH terms
- Interferon Regulatory Factor-4, Antigens, Neoplasm, Chromosomes, Human, Female, Follow-Up Studies, United Kingdom, Humans, Male, Middle Aged, Skin Pigmentation, Polymorphism, Single Nucleotide, Guanine Nucleotide Exchange Factors, Membrane Transport Proteins, White People, Ubiquitin-Protein Ligases, Interferon Regulatory Factors, Agouti Signaling Protein, Genome-Wide Association Study, Genetic Loci
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