gwas_catalog — GWAS Catalog variant-trait associations (2016-2026)

Description

Bipartite networks of genetic variants and the traits they are associated with, from the NHGRI-EBI Catalog of human genome-wide association studies (GWAS Catalog), which curates the associations reported in the published GWAS (with $p < 10^{-5}$) together with the details of the studies.

Nodes are variants (mostly single-nucleotide polymorphisms, identified by their dbSNP rsID, or by their position or another name when they have none) and traits (diseases, measurements and other phenotypes, as terms of the Experimental Factor Ontology, EFO, or of ontologies it imports, such as MONDO, HP, Orphanet or GO). There is an edge between a variant and a trait for each association reported in a study, so that a variant and a trait can be connected by several edges (e.g. associations found in several studies, or for several reported traits that are mapped to the same term). An association can involve several variants (haplotypes, written with ;, and interactions between variants, written with x) and several traits (a reported trait mapped to several terms): it then gives an edge between each of its variants and each of its traits. Associations that are not mapped to any trait term (up to 2% of the associations of a release) are kept: their trait is a node named by the trait as reported in the study (one node per distinct reported trait, without a term), marked by is_mapped false.

There is one network for each year from 2016 to 2026, from the last release of the year in the release archive of the catalog (which starts in March 2016): 2016-12-13, 2017-12-13, 2018-12-27, 2019-12-16, 2020-12-16, 2021-12-22, 2022-12-22, 2023-12-21, 2024-12-19, 2025-12-23 and 2026-10-22 (the latest one).

The networks have the following properties:

(Node) is_variant: whether the node is a variant (otherwise it is a trait).
(Node) is_mapped: whether the node is a trait mapped to an ontology term (false for the traits of the associations that are not mapped to any term, which are named by the reported trait, and for variants).
(Node) name: the identifier of the variant (e.g. rs4950928), or the name of the trait term (from the mappings of the reported traits of the same release; the name given in the associations if the term is not there), or the reported trait of the unmapped traits.
(Node) trait_uri: the URI of the trait term (e.g. http://www.ebi.ac.uk/efo/EFO_0000676; empty for variants and unmapped traits).
(Node) parent_trait: the category of the trait (e.g. Cancer, Cardiovascular disease, from the mappings of the reported traits; empty for variants).
(Node) chr_id, chr_pos, region: the chromosome, the position on the chromosome (in the genome assembly of the release) and the cytogenetic region of the variant (empty for traits, and for variants found only in associations of several variants).
(Node) mapped_gene: the genes mapped to the variant by the catalog (genes containing the variant, or the nearest upstream and downstream genes).
(Node) context: the functional class of the variant (e.g. intron_variant).
(Edge) study: the accession of the study (e.g. GCST000177).
(Edge) pubmed_id: the PubMed identifier of the publication of the study.
(Edge) date_added: the date at which the association was added to the catalog (as Unix time).
(Edge) reported_trait: the trait as reported in the study.
(Edge) snps: all the variants of the association, as given by the catalog.
(Edge) risk_allele: the strongest variant and risk allele (e.g. rs4950928-G; ? if the allele is unknown).
(Edge) risk_allele_frequency: the frequency of the risk allele in the controls (NaN if not given).
(Edge) p_value: the reported $p$-value of the association; p_value_mlog: $-\log_{10}$ of the $p$-value; p_value_text: additional information about the $p$-value (e.g. the subgroup).
(Edge) or_beta: the reported odds ratio, or the beta coefficient (NaN if not given); ci_text: the 95% confidence interval, and the unit of the beta coefficient.

Tags

Biological Genetic Unweighted Bipartite Multigraph Timestamps Metadata

Added

2026-10-31

Citation

M. Cerezo, E. Sollis, Y. Ji, E. Lewis, A. Abid, K. O. Bircan, P. Hall, J. Hayhurst, S. John, A. Mosaku, et al., "The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity." Nucleic Acids Research 53, D998-D1005 (2025) 10.1093/nar/gkae1070 Sci-Hub

Upstream URL OK

https://www.ebi.ac.uk/gwas/
https://ftp.ebi.ac.uk/pub/databases/gwas/releases/

Upstream license

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
2016	27,339	45,719	3.34	32.15	54.08	842.28	-0.17	17	0.86	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	1.5 MiB	1.9 MiB	1.9 MiB	1.9 MiB
2017	46,269	86,167	3.72	35.69	54.33	977.00	-0.19	19	0.90	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	2.7 MiB	3.4 MiB	3.4 MiB	3.4 MiB
2018	72,588	133,507	3.68	45.69	54.40	665.66	-0.20	17	0.94	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	4.2 MiB	5.4 MiB	5.3 MiB	5.3 MiB
2019	114,921	211,982	3.69	62.96	55.06	663.85	-0.20	18	0.97	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	6.6 MiB	8.5 MiB	8.3 MiB	8.4 MiB
2020	148,709	281,946	3.79	64.95	55.07	335.18	-0.23	15	0.97	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	8.8 MiB	11.3 MiB	11.0 MiB	11.5 MiB
2021	197,879	378,599	3.83	70.75	55.74	450.86	-0.29	17	0.98	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	12.1 MiB	15.5 MiB	15.1 MiB	15.6 MiB
2022	257,788	534,995	4.15	82.38	81.17	537.13	-0.31	18	0.98	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	16.4 MiB	21.1 MiB	20.5 MiB	21.8 MiB
2023	317,571	647,388	4.08	93.24	86.02	968.57	-0.22	17	0.98	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	19.8 MiB	25.8 MiB	25.1 MiB	26.6 MiB
2024	367,852	781,700	4.25	99.32	95.65	968.83	-0.21	17	0.98	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	23.8 MiB	31.0 MiB	30.1 MiB	32.3 MiB
2025	526,867	1,166,862	4.43	115.85	119.89	749.16	-0.17	16	0.98	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	34.6 MiB	45.2 MiB	43.9 MiB	47.3 MiB
2026	585,910	1,331,547	4.55	122.84	128.08	744.36	-0.18	16	0.99	Undirected	Bipartite	is_variant is_mapped name trait_uri parent_trait chr_id chr_pos region mapped_gene context	study pubmed_id date_added reported_trait snps risk_allele risk_allele_frequency p_value p_value_mlog p_value_text or_beta ci_text	39.5 MiB	51.5 MiB	50.1 MiB	54.3 MiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.