A global overview of pleiotropy and genetic architecture in complex traits
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Abstract
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 ).
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The GWAS Atlas has categorized many of the 405 UK Biobank traits, but because the GWAS Atlas uses different criteria for inclusion, some traits analyzed here were uncategorized.
“The GWAS Atlas has categorized many of the 405 UK Biobank traits; however, because the GWAS Atlas uses different criteria for inclusion into their database, some of the traits analyzed here were uncategorized.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [57]
The paper's Results (page not available in our copy) say the GWAS Atlas included UK Biobank traits and classified traits into 27 domains; its Methods describe criteria for inclusion. It does not identify the citing paper's 405 traits or establish that any of them were uncategorized because the two studies used different criteria. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe same genes/genetic variants are linked to different psychiatric conditions, addiction, and antisocial behavior, which can be explained by genes' pleiotropy in various complex traits.
“On the other hand, it was reported that the same genes/genetic variants were linked to different psychiatric conditions, addiction, and antisocial behavior (Ip et al., 2021; Antón-Galindo et al., 2023; Li et al., 2023; Wang et al., 2024; Pezzoli et al., 2025), which can be explained by genes’ pleiotropy in various complex traits (Watanabe et al., 2019).”
From Using polygenic scores to assess liability to antisocial behavior (2025) · cites this paper as Watanabe et al., 2019
There has been a remarkable increase in the last 15 years in the availability and sharing of genetic data, which enabled genome-wide association studies and characterization of the genetic architecture of complex human conditions and traits.
“Beyond oncology, there has been a remarkable increase in the last 15 years in the availability and sharing of genetic data, which enabled genome-wide association studies 12 and characterization of the genetic architecture of complex human conditions and traits 13 .”
From Multimodal biomedical AI (2022) · cites this paper as [13]
Pleiotropy is pervasive, as uncovered through genome-wide association studies.
“However, the topic has received renewed attention, given the pervasiveness of pleiotropy that has been uncovered through genome-wide association studies (GWAS) [8–10].”
From Multi-trait association studies discover pleiotropic loci between Alzheimer’s disease and cardiometabolic traits (2021) · cites this paper as [10]
In a PheWAS, traits associated with the introgressed haplotype (tagged by rs17544225) include monocyte count (P = 4 × 10−8) and monocyte percentage (P = 3 × 10−6; both pass the Bonferroni correction threshold 1 × 10−5).
“In a PheWAS, traits associated with the introgressed haplotype (tagged by rs17544225) include monocyte count (P = 4 × 10−8) and monocyte percentage (P = 3 × 10−6; both pass the Bonferroni correction threshold 1 × 10−5)57.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [57]
The ‘Pleiotropic SNPs’ section discusses associations for other SNPs, while the methods describe the paper’s broader GWAS analyses. Searches for rs17544225, an introgressed haplotype, monocyte count and percentage, and the stated P values found no passage in our copy reporting this PheWAS result. (LLM, conf=0.76)
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Chen, H., Liu, Y., Rui, X., Li, S., Sun, L., Xiao, G., Tang, H., Sun, Y., Guan, X., & Cao, C. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag1017
- Authors
- Watanabe, K., Stringer, S., Frei, O., Umićević Mirkov, M., de Leeuw, C., Polderman, T. J. C., van der Sluis, S., Andreassen, O. A., Neale, B. M., & Posthuma, D.
- Affiliations
- Amsterdam Neuroscience (NL)
- University of Oslo (NO)
- Oslo University Hospital (NO)
- Broad Institute (US)
- ORCID
- Venue
- Nature Genetics
- Published
- 2019-08-19
- Volume
- 51
- Issue
- 9
- Pages
- 1339-1348
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2969996045
- Cited by
- 1,332
- References
- 43
- Citations by year
- 2026: 146 · 2025: 215 · 2024: 230 · 2023: 214 · 2022: 210 · 2021: 187 · 2020: 98 · 2019: 29 · 2018: 3
- FWCI
- 83.92
- Type
- journal article
- Language
- en
- Update notices
- correction (2020-02-06)
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, other-oa)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
- VU Research Portal (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (453-14-005, 452-12-014)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- pleiotropy, genetic architecture, complex traits, genome-wide association study, polygenicity, causal variants, regulatory elements, coding variants, genetic discovery
- MeSH terms
- Genetics, Population, Humans, Phenotype, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study, Genetic Pleiotropy
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