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Abstract
Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10−9 at rs8018720 in SEC23A, and P = 1.9×10−14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene–gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.
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1 Program in Genetic Epidemiology and Statistical Genetics. Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA; Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
2 Department of Social Genetic & Developmental Psychiatry, King’s College London, Institute of Psychiatry, London, UK
3 Program in Genetic Epidemiology and Statistical Genetics. Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA; Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
4 Institute for Aging Research, Boston, MA, USA; Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA
5 Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, Québec, Canada
6 Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; Framingham Heart Study, Framingham, MA, USA
7 Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine Stanford, Stanford, CA, USA; Department of Medical Sciences, Uppsala University, Uppsala, Sweden
8 Institute for Aging Research, Boston, MA, USA
9 Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
10 Population, Policy and Practice, University College London, Great Ormond Street, Institute of Child Health, London, UK
11 Kidney Research Institute, Division of Nephrology, Seattle, WA, USA
12 MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
13 Department of Public Health & Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
14 Genetics and Personalized Medicine Program, University of Maryland School of Medicine, Baltimore, MD, USA
15 Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
16 Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
17 Department of Medicine, Indiana University, Endocrinology, Indianapolis, IN, USA
18 Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site, Greifswald, Berlin, Germany
19 DZHK (German Centre for Cardiovascular Research), Partner Site, Greifswald, Berlin, Germany; Institut für Community Medicine, SHIP/Klinisch-Epidemiologische Forschung, Universitätsmedizin Greifswald, Greifswald, Germany
20 Centre for Population Health Research, Sansom Institute for Health Research, University of South Australia, Adelaide, SA, Australia
21 Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
22 Division of Cardiology, Ciccarone Center for the Prevention of Heart Disease, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
23 Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
24 Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
25 Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
26 Erasmus MC Department of Epidemiology, Rotterdam, The Netherlands; AMC, Internal Medicine, Geriatrics Department, Amsterdam, The Netherlands
27 Department of Human Nutrition, Wageningen University, Wageningen, The Netherlands
28 Erasmus MC Department of Epidemiology, Rotterdam, The Netherlands
29 Vitamin K Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
30 Framingham Heart Study, Framingham, MA, USA
31 Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
32 Statistical and Translational Genetics, University of Helsinki, Helsinki 2U, Finland
33 Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
34 Department of Geriatric Medicine, University of Gothenburg and Sahlgrenska University Hospital, Mölndal, Sweden
35 Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, University of Helsinki, Tukholmankatu, Finland; Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
36 Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
37 Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
38 Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
39 Longitudinal Studies Section, Intramural Research Program of the National Institute on Aging, NIH, Baltimore, MD, USA
40 German Research Center for Environmental Health, Molecular Epidemiology, AME, Ingolstädter Landstr 1, Neuherberg, Germany
41 Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands
42 Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20, Leiden, The Netherlands; Max Planck Institute for Biology of Ageing, Köln (Cologne), Germany
43 Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
44 Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
45 Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Graz, Austria; SYNLAB Holding Deutschland GmbH, Augsburg, Germany
46 Division of Nephrology and Kidney Research Institute, University of Washington, Washington, DC, USA
47 USDA/ARS Children’s Nutrition Research Center, Houston, TX, USA
48 Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
49 Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
50 Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
51 Erasmus MC Department of Internal Medicine, Rotterdam, The Netherlands
52 Epidemiology and Biostatistics School of Public Health, Imperial College London, London, UK; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Aapistie 5A, Finland; Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, Finland
53 Population, Policy and Practice, University College London, Great Ormond Street, Institute of Child Health, London, UK; Centre for Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
54 Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
55 Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, the University of Edinburgh, Western General Hospital, Edinburgh, UK
56 MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, the University of Edinburgh, Western General Hospital, Edinburgh, UK
57 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
58 Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
59 Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands; Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
60 Erasmus MC Department of Epidemiology, Rotterdam, The Netherlands; Erasmus MC Department of Internal Medicine, Rotterdam, The Netherlands
61 Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin, University of Dublin, Dublin 24, Ireland
62 Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
63 Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
64 The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK; School of Medicine, University of Nottingham, Nottingham, UK
65 FIMM-Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
66 Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
67 Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
68 Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
69 Science Adviser at Academy of Finland, Helsinki, Finland
70 BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, University Avenue, Glasgow, UK
71 Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
72 Vitas AS, Oslo, Norway
73 Department of Public Health & Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
74 The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK
75 Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville, TN, USA
76 Population, Policy and Practice, University College London, Great Ormond Street, Institute of Child Health, London, UK; Centre for Population Health Research, Sansom Institute for Health Research, University of South Australia, Adelaide, SA, Australia
77 Program in Genetic Epidemiology and Statistical Genetics. Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA