Training & Related resources
GWAS Catalog training materials
EBI Train online
New to the Catalog? Start here with GWAS Catalog - Exploring SNP-trait associations, an easily accessible interactive tutorial on the full range of features the GWAS Catalog has to offer.
Training videos
Recorded webinars are available to guide you through different aspects of the Catalog:
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Exploring genotype-phenotype data using the GWAS Catalog (2022) for an introduction to the GWAS Catalog and a demonstration of our web-based search interface.
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Data submission for genome-wide association studies at the GWAS Catalog (2023) for a detailed walkthrough of our summary statistics submission system.
Earlier webinars are also available:
In-person training materials
Training materials from in-person training workshops held by the GWAS Catalog team are available on Github and our FTP server. If you would like to make use of these slides, please cite the GWAS Catalog as detailed on the About page.
Publications
GWAS Catalog publications
Current GWAS Catalog citation: Cerezo et al, 2025 https://doi.org/10.1093/nar/gkae1070 Nucleic Acids Research, Volume 53, Issue D1, Pages D998–D1005
Older resource update papers:
Sollis et al, 2023 https://doi.org/10.1093/nar/gkac1010. Nucleic Acids Research 51(D1):D977-D985
Buniello, MacArthur et al, 2019 https://doi.org/10.1093/nar/gky1120. Nucleic Acids Research, 2019, Vol. 47 (Database issue): D1005-D1012.
MacArthur et al, 2017 https://doi.org/10.1093/nar/gkw1133. Nucleic Acids Research, Vol. 45 (Database issue): D896-D901.
Welter D et al, 2014 https://doi.org/10.1093/nar/gkt1229. Nucleic Acids Research, Vol. 42 (Database issue): D1001-D1006.
Other GWAS Catalog papers:
Harris et al, 2024 Genome-wide association testing beyond SNPs. Nature Reviews Genetics. 2024 Oct 7. Epub ahead of print.
MacArthur et al, 2021 Workshop proceedings: GWAS Catalog standards and sharing. Cell Genomics Vol. 1, Issue 1, 100004.
McMahon et al, 2021 Sequencing-based genome-wide association studies reporting standards. Cell Genomics Vol. 1, issue 1, 100005.
Morales et al, 2017 A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biology, 19:21.
Hindorff LA, et al 2009 Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA, 2009, 106, 9362–9367.
Papers with GWAS Catalog contribution:
Costanzo et al, 2025 Realizing the promise of genome-wide association studies for effector gene prediction, Nature Genetics, Volume 57:1578–1587, May 2025.
Matentzoglu et al, 2025 The Unified Phenotype Ontology : a framework for cross-species integrative phenomics, Genetics, Volume 229, Issue 3, March 2025
Lambert, Wingfield et al, 2024. Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. 56(10):1989-1994, Oct 2024.
Stefancik et al, 2023 The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences. Mammalian Genome 34, 364–378.
Lambert et al, 2021 The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics volume 53, pages420–425.
Lee K et al, 2018 Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Computational Biology 14(8):e1006390.
Other background reading
Uffelmann et al, 2021 Genome-wide association studies. Nat Rev Methods Primers 1, 59.
A beginners guide to GWAS (2016)
What is an Ontology? (2010)
Abdellaoui et al, 2023. 15 years of GWAS discovery: Realizing the promise. Am J Hum Genet. 2023 Feb 2;110(2):179-194.
Visscher et al, 2017 10 Years of GWAS Discovery: Biology, Function and Translation AJHG Volume 101, Issue 1, 6 July 2017, Pages 5-22
Manolio, 2010 Genomewide Association Studies and assessment of the risk of disease NEJM 363:166-176
News posts
Trait annotation in the GWAS Catalog (2021): a discussion of how traits are annotated in the GWAS Catalog, focussing on improved background trait annotation.
Sharing is caring: why we need more freely available cancer GWAS summary statistics (2021): a blog post calling for more freely available cancer GWAS summary statistics.
Ten years of the GWAS Catalog – Past, present and future(2018): 10th Anniversary blog post highlighting the links between the GWAS Catalog and Ensembl.
Everything you need to know about the new GWAS Catalog (2018): a blog post describing the collaboration between the GWAS Catalog and Open Targets.
Or see the full index.
Useful resources
Tools & data services
| gwasrapidd | an R package to query, download and wrangle GWAS Catalog data |
| pandasgwas | A Python package for retrieval of GWAS Catalog data |
| Variant Effect Predictor (VEP) | Determines the effect of variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions |
| Phenoscanner | Tool to facilitate “phenome scans”, the cross-referencing of genetic variants with a broad range of phenotypes, using a range of data sources including GWAS, eQTL and metabolite data |
| HuGE Navigator | Knowledge base in human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions |
| Phenotype-Genotype Integrator | Merges GWAS Catalog Data with other NCBI databases to facilitate prioritisation of GWAS hits for follow-up |
| PGS Catalog | An open database of polygenic scores and the relevant metadata required for accurate application and evaluation |
| Open Targets Platform | Platform for the identification of drug targets using multiple data types including GWAS |
| Target Illumination GWAS Analytics (TIGA) | Resource for drug target illumination by scoring and ranking protein-coding genes associated with traits from GWAS |
| LocusZoom | A suite of software for creating regional association plots from GWAS data |
| Elixir Tools and Data Services Registry | A registry of GWAS-related resources and tools |
| OMICStools | Searchable database of GWAS and other bioinformatics tools |
| Pharos | Pharos is the user interface to the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) program |
| GWAS Diversity Monitor | Interactive dashboard monitoring the diversity of participants across all published GWAS |
Resources used within the GWAS Catalog
For more information on how we use these resources, see our Methods page.
| Experimental Factor Ontology (EFO) | The ontology used for trait mapping in the GWAS Catalog |
| Ensembl Genome Browser | Genome browser and data for vertebrate genomes, used in our variant mapping pipeline. Ensembl annotates genes, computes multiple alignments, predicts regulatory function and collects disease data |
| PubMed | Literature search and citation annotation |
| EuropePMC | Literature search and citation annotation |
| CIA Factbook | A rich source of population demographic data, used by curators |
| NCBI | Data used for variant mapping in older versions of the Catalog |
Genome and phenome resources
| 1000 Genomes | The largest public reference catalogue of worldwide human variation and genotype data |
| International HapMap Project | The first public catalogue of human variation data, now superseded by 1000Genomes |
| UCSC Genome Browser | Genome browser to interactively visualize genomic data |
| PhenX toolkit | Consensus measures of Phenotypes and eXposures |
| dbSNP | Database of human single nucleotide polymorphisms |
| National Centre for Biotechnology Information | Provides wide range of resources including Entrez gene, GenBank, PubMed and ClinVar |
Sources of summary statistics
Summary statistics are available via the GWAS Catalog where possible. Find additional sources of summary statistics here.
Community workshops
Materials from our community workshop on standards and infrastructure for predicted effector gene lists, a collaboration between the GWAS Catalog, HuGEAMP Knowledge Portal Network and Open Targets, are available online.
Materials from our community workshop on GWAS summary statistics standards and sharing, held in June 2020 to address the standards, infrastructure and incentives required to promote and enable broader sharing of data, are available here and are published as MacArthur et al, 2021 Workshop proceedings: GWAS Catalog standards and sharing, Cell Genomics 1(1).