DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genome-wide Association Study for Vitamin D Levels Reveals 69 Independent Loci

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Sponsoring Org.:
USDOE Office of Electricity (OE), Advanced Grid Research & Development. Power Systems Engineering Research
OSTI Identifier:
1872667
Resource Type:
Published Article
Journal Name:
American Journal of Human Genetics
Additional Journal Information:
Journal Name: American Journal of Human Genetics Journal Volume: 106 Journal Issue: 3; Journal ID: ISSN 0002-9297
Publisher:
Elsevier
Country of Publication:
United States
Language:
English

Citation Formats

Manousaki, Despoina, Mitchell, Ruth, Dudding, Tom, Haworth, Simon, Harroud, Adil, Forgetta, Vincenzo, Shah, Rupal L., Luan, Jian’an, Langenberg, Claudia, Timpson, Nicholas J., and Richards, J. Brent. Genome-wide Association Study for Vitamin D Levels Reveals 69 Independent Loci. United States: N. p., 2020. Web. doi:10.1016/j.ajhg.2020.01.017.
Manousaki, Despoina, Mitchell, Ruth, Dudding, Tom, Haworth, Simon, Harroud, Adil, Forgetta, Vincenzo, Shah, Rupal L., Luan, Jian’an, Langenberg, Claudia, Timpson, Nicholas J., & Richards, J. Brent. Genome-wide Association Study for Vitamin D Levels Reveals 69 Independent Loci. United States. https://doi.org/10.1016/j.ajhg.2020.01.017
Manousaki, Despoina, Mitchell, Ruth, Dudding, Tom, Haworth, Simon, Harroud, Adil, Forgetta, Vincenzo, Shah, Rupal L., Luan, Jian’an, Langenberg, Claudia, Timpson, Nicholas J., and Richards, J. Brent. Sun . "Genome-wide Association Study for Vitamin D Levels Reveals 69 Independent Loci". United States. https://doi.org/10.1016/j.ajhg.2020.01.017.
@article{osti_1872667,
title = {Genome-wide Association Study for Vitamin D Levels Reveals 69 Independent Loci},
author = {Manousaki, Despoina and Mitchell, Ruth and Dudding, Tom and Haworth, Simon and Harroud, Adil and Forgetta, Vincenzo and Shah, Rupal L. and Luan, Jian’an and Langenberg, Claudia and Timpson, Nicholas J. and Richards, J. Brent},
abstractNote = {},
doi = {10.1016/j.ajhg.2020.01.017},
journal = {American Journal of Human Genetics},
number = 3,
volume = 106,
place = {United States},
year = {Sun Mar 01 00:00:00 EST 2020},
month = {Sun Mar 01 00:00:00 EST 2020}
}

Works referenced in this record:

PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations
journal, June 2019


The role of vitamin D in reducing cancer risk and progression
journal, April 2014

  • Feldman, David; Krishnan, Aruna V.; Swami, Srilatha
  • Nature Reviews Cancer, Vol. 14, Issue 5
  • DOI: 10.1038/nrc3691

A role for vitamin D and omega-3 fatty acids in major depression? An exploration using genomics
journal, September 2019

  • Milaneschi, Yuri; Peyrot, Wouter J.; Nivard, Michel G.
  • Translational Psychiatry, Vol. 9, Issue 1
  • DOI: 10.1038/s41398-019-0554-y

The impact of a fine-scale population stratification on rare variant association test results
journal, December 2018


Nutritional Factors and Preservation of C-Peptide in Youth With Recently Diagnosed Type 1 Diabetes
journal, June 2013

  • Mayer-Davis, Elizabeth J.; Dabelea, Dana; Crandell, Jamie L.
  • Diabetes Care, Vol. 36, Issue 7
  • DOI: 10.2337/dc12-2084

GWAMA: software for genome-wide association meta-analysis
journal, May 2010


Effect of Genetically Low 25-Hydroxyvitamin D on Mortality Risk: Mendelian Randomization Analysis in 3 Large European Cohorts
journal, January 2019

  • Aspelund, Thor; Grübler, Martin R.; Smith, Albert V.
  • Nutrients, Vol. 11, Issue 1
  • DOI: 10.3390/nu11010074

Vitamin D supplement in early childhood and risk for Type I (insulin-dependent) diabetes mellitus
journal, January 1999


Intake of vitamin D and risk of type 1 diabetes: a birth-cohort study
journal, November 2001


An atlas of genetic correlations across human diseases and traits
journal, September 2015

  • Bulik-Sullivan, Brendan; Finucane, Hilary K.; Anttila, Verneri
  • Nature Genetics, Vol. 47, Issue 11
  • DOI: 10.1038/ng.3406

Partitioning heritability by functional annotation using genome-wide association summary statistics
journal, September 2015

  • Finucane, Hilary K.; Bulik-Sullivan, Brendan; Gusev, Alexander
  • Nature Genetics, Vol. 47, Issue 11
  • DOI: 10.1038/ng.3404

Mendelian Randomization Analysis With Multiple Genetic Variants Using Summarized Data
journal, September 2013

  • Burgess, Stephen; Butterworth, Adam; Thompson, Simon G.
  • Genetic Epidemiology, Vol. 37, Issue 7
  • DOI: 10.1002/gepi.21758

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci
journal, March 2016

  • Ellinghaus, David; Jostins, Luke; Spain, Sarah L.
  • Nature Genetics, Vol. 48, Issue 5
  • DOI: 10.1038/ng.3528

Investigating causality in the association between vitamin D status and self-reported tiredness
journal, February 2019


Polymorphic Human Sulfotransferase 2A1 Mediates the Formation of 25-Hydroxyvitamin D 3 -3- O -Sulfate, a Major Circulating Vitamin D Metabolite in Humans
journal, January 2018

  • Wong, Timothy; Wang, Zhican; Chapron, Brian D.
  • Drug Metabolism and Disposition, Vol. 46, Issue 4
  • DOI: 10.1124/dmd.117.078428

Effect of vitamin D supplementation on non-skeletal disorders: a systematic review of meta-analyses and randomised trials
journal, December 2017


Circulating vitamin D concentrations and risk of breast and prostate cancer: a Mendelian randomization study
journal, December 2018

  • Jiang, Xia; Dimou, Niki L.; Al-Dabhani, Kawthar
  • International Journal of Epidemiology, Vol. 48, Issue 5
  • DOI: 10.1093/ije/dyy284

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
journal, April 2018


Integrating predicted transcriptome from multiple tissues improves association detection
journal, January 2019


Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis
journal, November 2015

  • Loh, Po-Ru; Bhatia, Gaurav; Gusev, Alexander
  • Nature Genetics, Vol. 47, Issue 12
  • DOI: 10.1038/ng.3431

Genome-wide association study of circulating vitamin D levels
journal, April 2010

  • Ahn, Jiyoung; Yu, Kai; Stolzenberg-Solomon, Rachael
  • Human Molecular Genetics, Vol. 19, Issue 13
  • DOI: 10.1093/hmg/ddq155

Is there a causal relationship between vitamin D and melanoma risk? A Mendelian randomization study
journal, September 2019

  • Liyanage, U. E.; Law, M. H.; Barrett, J. H.
  • British Journal of Dermatology, Vol. 182, Issue 1
  • DOI: 10.1111/bjd.18238

Vitamin D and its emerging role in immunopathology
journal, October 2011


Genetic and non-genetic correlates of vitamins K and D
journal, November 2007

  • Shea, M. K.; Benjamin, E. J.; Dupuis, J.
  • European Journal of Clinical Nutrition, Vol. 63, Issue 4
  • DOI: 10.1038/sj.ejcn.1602959

Reference-based phasing using the Haplotype Reference Consortium panel
journal, October 2016

  • Loh, Po-Ru; Danecek, Petr; Palamara, Pier Francesco
  • Nature Genetics, Vol. 48, Issue 11
  • DOI: 10.1038/ng.3679

Vitamin D deficiency in early life accelerates Type 1 diabetes in non-obese diabetic mice
journal, March 2004


‘Mendelian randomization’: can genetic epidemiology contribute to understanding environmental determinants of disease?*
journal, February 2003

  • Davey Smith, George; Ebrahim, Shah
  • International Journal of Epidemiology, Vol. 32, Issue 1
  • DOI: 10.1093/ije/dyg070

Genotype imputation for genome-wide association studies
journal, June 2010

  • Marchini, Jonathan; Howie, Bryan
  • Nature Reviews Genetics, Vol. 11, Issue 7
  • DOI: 10.1038/nrg2796

Estimation of effect size distribution from genome-wide association studies and implications for future discoveries
journal, June 2010

  • Park, Ju-Hyun; Wacholder, Sholom; Gail, Mitchell H.
  • Nature Genetics, Vol. 42, Issue 7
  • DOI: 10.1038/ng.610

Phenome-wide Mendelian-randomization study of genetically determined vitamin D on multiple health outcomes using the UK Biobank study
journal, September 2019

  • Meng, Xiangrui; Li, Xue; Timofeeva, Maria N.
  • International Journal of Epidemiology, Vol. 48, Issue 5
  • DOI: 10.1093/ije/dyz182

METAL: fast and efficient meta-analysis of genomewide association scans
journal, July 2010


Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis
journal, August 2017

  • Manousaki, Despoina; Dudding, Tom; Haworth, Simon
  • The American Journal of Human Genetics, Vol. 101, Issue 2
  • DOI: 10.1016/j.ajhg.2017.06.014

Incidence of Type 2 diabetes in England and its association with baseline impaired fasting glucose: The Ely study 1990-2000
journal, February 2007


Biological interpretation of genome-wide association studies using predicted gene functions
journal, January 2015

  • Pers, Tune H.; Karjalainen, Juha M.; Chan, Yingleong
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms6890

Undiagnosed Glucose Intolerance in the Community: the Isle of Ely Diabetes Project
journal, January 1995


GCTA: A Tool for Genome-wide Complex Trait Analysis
journal, January 2011

  • Yang, Jian; Lee, S. Hong; Goddard, Michael E.
  • The American Journal of Human Genetics, Vol. 88, Issue 1
  • DOI: 10.1016/j.ajhg.2010.11.011

Evidence for a causal relationship between low vitamin D, high BMI, and pediatric-onset MS
journal, March 2017


Vitamin D and Inflammatory Bowel Disease: Mendelian Randomization Analyses in the Copenhagen Studies and UK Biobank
journal, June 2018

  • Lund-Nielsen, Josephine; Vedel-Krogh, Signe; Kobylecki, Camilla Jannie
  • The Journal of Clinical Endocrinology & Metabolism, Vol. 103, Issue 9
  • DOI: 10.1210/jc.2018-00250

Circulating Calcitriol Concentrations and Total Mortality
journal, June 2009


Circulating serum vitamin D levels and total body bone mineral density: A Mendelian randomization study
journal, January 2019

  • Sun, Jing-yi; Zhao, Ming; Hou, Yajun
  • Journal of Cellular and Molecular Medicine, Vol. 23, Issue 3
  • DOI: 10.1111/jcmm.14153

Vitamin D and the Risk of Depression: A Causal Relationship? Findings from a Mendelian Randomization Study
journal, May 2019

  • Libuda, Lars; Laabs, Björn-Hergen; Ludwig, Christine
  • Nutrients, Vol. 11, Issue 5
  • DOI: 10.3390/nu11051085

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia
journal, March 2016

  • Galinsky, Kevin J.; Bhatia, Gaurav; Loh, Po-Ru
  • The American Journal of Human Genetics, Vol. 98, Issue 3
  • DOI: 10.1016/j.ajhg.2015.12.022

Vitamin D and Risk of Multiple Sclerosis: A Mendelian Randomization Study
journal, August 2015


Serum 25-Hydroxyvitamin D Concentrations and Major Depression: A Mendelian Randomization Study
journal, December 2018

  • Michaëlsson, Karl; Melhus, Håkan; Larsson, Susanna
  • Nutrients, Vol. 10, Issue 12
  • DOI: 10.3390/nu10121987

Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase
journal, May 2004

  • Cheng, Jeffrey B.; Levine, Michael A.; Bell, Norman H.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 20
  • DOI: 10.1073/pnas.0402490101

Common genetic determinants of vitamin D insufficiency: a genome-wide association study
journal, July 2010


Mendelian randomization shows a causal effect of low vitamin D on multiple sclerosis risk
journal, September 2016


Low Levels of 25-hydroxyvitamin D 3 and 1,25-dihydroxyvitamin D 3 in Patients with Newly Diagnosed Type 1 Diabetes
journal, November 2005

  • Pozzilli, P.; Manfrini, S.; Crinò, A.
  • Hormone and Metabolic Research, Vol. 37, Issue 11
  • DOI: 10.1055/s-2005-870578

Reassessing the Association between Circulating Vitamin D and IGFBP-3: Observational and Mendelian Randomization Estimates from Independent Sources
journal, December 2018

  • Tan, Vanessa Y.; Biernacka, Kalina M.; Dudding, Tom
  • Cancer Epidemiology, Biomarkers & Prevention, Vol. 27, Issue 12
  • DOI: 10.1158/1055-9965.EPI-18-0113

The UK Biobank resource with deep phenotyping and genomic data
journal, October 2018


Genetic Contribution to Bone Metabolism, Calcium Excretion, and Vitamin D and Parathyroid Hormone Regulation
journal, February 2001


Serum Parathyroid Hormone, 25-Hydroxyvitamin D, and Risk of Alzheimer’s Disease: A Mendelian Randomization Study
journal, September 2018

  • Larsson, Susanna; Traylor, Matthew; Markus, Hugh
  • Nutrients, Vol. 10, Issue 9
  • DOI: 10.3390/nu10091243

Potential causal associations of serum 25-hydroxyvitamin D with lipids: a Mendelian randomization approach of the HUNT study
journal, November 2018

  • Mai, Xiao-Mei; Videm, Vibeke; Sheehan, Nuala A.
  • European Journal of Epidemiology, Vol. 34, Issue 1
  • DOI: 10.1007/s10654-018-0465-x

No Association Between Vitamin D Status and Risk of Barrett's Esophagus or Esophageal Adenocarcinoma: A Mendelian Randomization Study
journal, October 2019

  • Dong, Jing; Gharahkhani, Puya; Chow, Wong-Ho
  • Clinical Gastroenterology and Hepatology, Vol. 17, Issue 11
  • DOI: 10.1016/j.cgh.2019.01.041

Serum 25-Hydroxyvitamin D Concentrations and Ischemic Stroke and Its Subtypes: A Mendelian Randomization Study
journal, October 2018


Heritability and seasonal variability of vitamin D concentrations in male twins
journal, October 2010

  • Karohl, Cristina; Su, Shaoyong; Kumari, Meena
  • The American Journal of Clinical Nutrition, Vol. 92, Issue 6
  • DOI: 10.3945/ajcn.2010.30176

Skeletal and Extraskeletal Actions of Vitamin D: Current Evidence and Outstanding Questions
journal, October 2018

  • Bouillon, Roger; Marcocci, Claudio; Carmeliet, Geert
  • Endocrine Reviews, Vol. 40, Issue 4
  • DOI: 10.1210/er.2018-00126

Vitamin D dose response is underestimated by Endocrine Society's Clinical Practice Guideline
journal, June 2013

  • McKenna, Malachi J.; Murray, Barbara F.
  • Endocrine Connections, Vol. 2, Issue 2
  • DOI: 10.1530/EC-13-0008

The Ensembl Variant Effect Predictor
journal, June 2016


Vitamin D levels and risk of delirium: A mendelian randomization study in the UK Biobank
journal, February 2019


Vitamin D Levels in Subjects With and Without Type 1 Diabetes Residing in a Solar Rich Environment
journal, August 2009

  • Bierschenk, Lindsey; Alexander, John; Wasserfall, Clive
  • Diabetes Care, Vol. 32, Issue 11
  • DOI: 10.2337/dc09-1089

An atlas of genetic influences on osteoporosis in humans and mice
journal, December 2018


Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
journal, January 2018