After a decade of genome-wide association studies (GWASs), fundamental questions in human genetics, such as the extent of pleiotropy across the genome and variation in genetic architecture across traits, are still unanswered. The current availability of hundreds of GWASs provides a unique opportunity to address these questions. We systematically analyzed 4,155 publicly available GWASs. For a subset of well-powered GWASs on 558 traits, we provide an extensive overview of pleiotropy and genetic architecture. We show that trait-associated loci cover more than half of the genome, and 90% of these overlap with loci from multiple traits. We find that potential causal variants are enriched in coding and flanking regions, as well as in regulatory elements, and show variation in polygenicity and discoverability of traits. Our results provide insights into how genetic variation contributes to trait variation. All GWAS results can be queried and visualized at the GWAS ATLAS resource (https://atlas.ctglab.nl).
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
All publicly available GWAS summary statistics (original) files curated in this study are accessible from the original links provided at https://atlas.ctglab.nl. GWAS summary statistics for 600 traits from UK Biobank performed in this study are also provided at https://atlas.ctglab.nl and an archived file will be made available upon publication from https://ctg.cncr.nl/software/summary_statistics.
Edwards, A. O. et al. Complement factor H polymorphism and age-related macular degeneration. Science 308, 421–425 (2005).
Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001–D1006 (2014).
Lander, E. S. Initial impact of the sequencing of the human genome. Nature 470, 187–197 (2011).
Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017).
Henderson, P. & Stevens, C. The role of autophagy in Crohn’s disease. Cells 1, 492–519 (2012).
Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376–381 (2014).
Gaulton, K. J. et al. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci. Nat. Genet. 47, 1415–1425 (2015).
Canela-Xandri, O., Rawlik, K. & Tenesa, A. An atlas of genetic associations in UK Biobank. Nat. Genet. 50, 1593–1599 (2018).
Timpson, N. J., Greenwood, C. M. T., Soranzo, N., Lawson, D. J. & Richards, J. B. Genetic architecture: the shape of the genetic contribution to human traits and disease. Nat. Rev. Genet. 19, 110–124 (2018).
Boyle, E. A., Li, Y. I. & Pritchard, J. K. An expanded view of complex traits: from polygenic to omnigenic. Cell 169, 1177–1186 (2017).
Wray, N. R., Wijmenga, C., Sullivan, P. F., Yang, J. & Visscher, P. M. Common disease is more complex than implied by the core gene omnigenic model. Cell 173, 1573–1580 (2018).
Bycroft, C. et al. The UK Biobank resource with deep phenotyping and genomic data. Nature 562, 203–209 (2018).
Goh, K. et al. The human disease network. Proc. Natl Acad. Sci. USA 104, 8685–8690 (2007).
Polderman, T. J. C. et al. Meta-analysis of the heritability of human traits based on fifty years of twin studies. Nat. Genet. 47, 702–709 (2015).
Mahajan, A. et al. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps. Nat. Genet. 50, 1505–1513 (2018).
de Leeuw, C. A., Mooij, J. M., Heskes, T. & Posthuma, D. MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput. Biol. 11, e1004219 (2015).
Bulik-sullivan, B. K. et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291–295 (2015).
Solovieff, N., Cotsapas, C., Lee, P. H., Purcell, S. M. & Smoller, J. W. Pleiotropy in complex traits: challenges and strategies. Nat. Rev. Genet. 14, 483–495 (2013).
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
The GTEx Consortium. Genetic effects on gene expression across human tissues. Nature 550, 204–213 (2017).
Zhu, Z. et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat. Genet. 48, 481–487 (2016).
Manolio, T. A. et al. Finding the missing heritability of complex diseases. Nature 461, 747–753 (2009).
Lee, S., Abecasis, G. R., Boehnke, M. & Lin, X. Rare-variant association analysis: study designs and statistical tests. Am. J. Hum. Genet. 95, 5–23 (2014).
van de Bunt, M., Cortes, A., Brown, M. A., Morris, A. P. & McCarthy, M. I. Evaluating the performance of fine-mapping strategies at common variant GWAS loci. PLoS Genet. 11, e1005535 (2015).
Benner, C. et al. FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics 32, 1493–1501 (2016).
Speed, D. et al. Reevaluation of SNP heritability in complex human traits. Nat. Genet. 49, 986–992 (2017).
Speed, D. & Balding, D. J. SumHer better estimates the SNP heritability of complex traits from summary statistics. Nat. Genet. 51, 277–284 (2019).
Holland, D. et al. Beyond SNP heritability: polygenicity and discoverability estimated for multiple phenotypes with a univariate gaussian mixture model. Preprint at https://doi.org/10.1101/133132 (2018).
Frei, O. et al. Bivariate causal mixture model quantifies polygenic overlap between complex traits beyond genetic correlation. Nat. Commun. 10, 2417 (2019).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Watanabe, K., Taskesen, E., van Bochoven, A. & Posthuma, D. Functional mapping and annotation of genetic associations with FUMA. Nat. Commun. 8, 1826 (2017).
Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 27, 1739–1740 (2011).
Zheng, J. et al. LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics 33, 272–279 (2017).
Yengo, L. et al. Meta-analysis of genome-wide association studies for height and body mass index in ∼700,000 individuals of European ancestry. Hum. Mol. Genet. 27, 3641–3649 (2018).
Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
Visscher, P. M. et al. Statistical power to detect genetic (co)variance of complex traits using SNP data in unrelated samples. PLoS Genet. 10, e1004269 (2014).
Benner, C. et al. Prospects of fine-mapping trait-associated genomic regions by using summary statistics from genome-wide association studies. Am. J. Hum. Genet. 101, 539–551 (2017).
Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015).
Tak, Y. G. & Farnham, P. J. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin 8, 57 (2015).
We thank all consortiums and all other individual laboratories for making GWAS summary statistics publicly available. We also thank P. Visscher and N. Wray for their thoughtful suggestions and discussions. We additionally thank A. Dale for his suggestions. This work was funded by the Netherlands Organization for Scientific Research (grant nos. NWO VICI 453-14-005 and NWO VIDI 452-12-014).
The authors declare no competing interests.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Watanabe, K., Stringer, S., Frei, O. et al. A global overview of pleiotropy and genetic architecture in complex traits. Nat Genet 51, 1339–1348 (2019). https://doi.org/10.1038/s41588-019-0481-0
A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density
Cell Metabolism (2021)
Alcohol and cigarette smoking consumption as genetic proxies for alcohol misuse and nicotine dependence
Drug and Alcohol Dependence (2021)
Bayesian meta‐analysis models for cross cancer genomic investigation of pleiotropic effects using group structure
Statistics in Medicine (2021)
The American Journal of Human Genetics (2021)