Several resources are used to generate the GWAS diagram browser. Some of the files available for download are listed below.
This section aims to provide some guidance on how to use the new dynamic GWAS diagram. For an introduction to the GWAS catalog, see the "About" tab.
To view all the SNPs associated with any trait in a given location, simply click on the trait you are interested in. An interactive pop-up will display the SNPs for that trait, the p-value for each SNP-trait association, the study in which the association was identified, the trait assigned by the GWAS catalog curators and the EFO term the SNP-trait association is mapped to. The SNP, EFO term and study fields are interactive, linking out to Ensembl, EFO and UKPMC, respectively. There is also a link to the entry for this SNP in the GWAS catalog. The pop-up can be moved around the screen. Clicking on another trait automatically closes the current pop-up. Alternatively, close the pop-up by clicking on the cross in its top right corner.
The full diagram can be filtered by typing a trait into the text box above the diagram and hitting "Enter" or clicking the "Query" button.
If the trait you are interested in is not available in the Downloads tab, you can create a custom diagram by filtering the main diagram according to you chosen trait, then taking a screen shot of the resulting image.
A legend of the colour scheme is available in the "Legend" box in the top right corner of the diagram. Simply click on the box to expand ("Show legend") or hide ("Hide legend") the legend. Click on any link in the legend to filter the diagram by that category. This does not work for any of the "other"-type categories (other measurement, other disease and other trait).
Chromosomes and traits (coloured circles) have labels that display when hovering the mouse pointer over a given element. The displayed labels correspond to the EFO term mapped this SNP.
The diagram was designed to have a GoogleMaps-style interactivity.
There are two ways to zoom in and out. The easiest option is to use the
scroll wheel on the mouse or touch pad on a laptop. Scrolling up zooms in and scrolling down zooms out.
This feature may not work with all touch pads. Alternatively, the left-hand side of the diagram features
a zoom bar which can be used to generate exactly the same effect, by dragging the little square up or
down the bar with the mouse pointer. The zoom bar occasionally appears in the wrong place. This is a
known bug. Refreshing the browser window usually solves the problem.
The diagram can be moved around the viewing area by clicking on any part of the diagram with the left mouse button and, holding the mouse button down, dragging the diagram around the screen until the desired part is visible. This feature is particularly useful for centering the diagram on a specific location at higher zoom levels.
Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., and Parkinson, H. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations Nucl. Acids Res. 42 (D1): D1001-D1006. doi: 10.1093/nar/gkt1229
For questions, feature requests or bug reports, please contact the GWAS team at EBI. In particular, please let us know if a given feature does not behave as described. Always specify in which web browser, including which version, and which operating system the problem occurred. This application is tested in all the latest versions of Mozilla Firefox, Google Chrome, Safari and Internet Explorer. If you find an older browser version which does not work, please let us know. In this event, click here for a static version of the diagram in PNG format.
The GWAS Catalog data is extracted from the literature. Extracted information includes publication information, study cohort information such as cohort size, country of recruitment and subject ethnicity, and SNP-disease association information including SNP identifier (i.e. RSID), p-value, gene and risk allele. Each study is also assigned a trait that best represents the phenotype under investigation. When multiple traits are analysed in the same study either multiple entries are created, or individual SNPs are annotated with their specific traits. Traits are used both to query and visualise the data in the Catalog's web form and diagram-based query interfaces.
Data extraction and curation for the GWAS Catalog is an expert activity; each step is performed by scientists supported by a web-based tracking and data entry system which allows multiple curators to search, annotate, verify and publish the Catalog data. Papers that qualify for inclusion in the Catalog are identified through weekly PubMed searches. They then undergo two levels of curation. First all data, including association information for SNPs, traits and general information about the study, are extracted by one curator. second curator then performs an additional round of curation to double-check the accuracy and consistency of all the information. Finally, an automated pipeline run at the NCBI performs checks for missing information, such as SNP identifiers, resolution of the citation in PubMed, existence of SNPs in dbSNP, confirmation of gene names vs. NCBI's Gene database, confirmation that the reported SNP and gene are in the same chromosomal region, as well as adding additional information such as the SNP's base pair and cytogenetic location in the current human genome reference assembly. This information is then used for queries and in the production of the karyotype diagram.
The National Human Genome Research Institute (NHGRI) Catalog of Published Genome-Wide Association Studies or GWAS catalogue provides a quality controlled, manually curated, literature-derived collection of all published GWA studies assaying at least 100,000 SNPs and all SNP-trait associations with p-values < 1.0 × 10-5 (Hindorff et al., 2009). The catalogue can be searched by a number of options including journal, first author, trait, chromosomal region, gene, SNP, odds ratio and p-value threshold. As of 16/12/13, it includes 1778 publications and 12123 SNPs. In addition to the SNP-trait association data, the catalogue also publishes the iconic GWAS diagram of all SNP-trait associations, with p-values ≤ 5.0 × 10-8, mapped to the SNPs’ chromosomal locations. The diagram is released quarterly and the latest version of the diagram is made available on the GWAS catalogue website in PDF format and as a PowerPoint slide.
This page hosts a novel system that generates the GWAS diagram dynamically using semantic web technologies. The diagram produced in this fashion can be filtered and searched at different levels of granularity and by different criteria, currently including trait (main diagram tab) and publication date (time series tab, currently availabe for a fixed set of time points only). It is possible to zoom in over chromosomes in order to see all SNP-trait associations for a given region. SNP-trait associations are fully interactive, with trait name information is available on mouse-over and traits being clickable to allow proceeding from an association to the catalogue entry, to the publication as well as to Ensembl for further information.
The diagram is generated in SVG (Scalable Vector Graphics) as a web application with a Java back-end using an Apache Tomcat server. The catalogue data is presented as a knowledge base, based on the GWAS Catalog schema ontology, which formalises the relationship between various concepts such as SNP, trait and study. Both the knowledge base and the schema ontology can be found in the "Downloads" tab. The traits in the GWAS catalog are formalised by mapping each trait to one or more terms in the Experimental Factor Ontology (EFO). Mapping traits to an ontology provides querying capabilities across multiple traits and trait categories. In the case of cancer for example, a single query can identify all traits related to cancer whereas in the GWAS catalog, such a query would require each cancer-related trait to be selected manually. The EFO-driven SNP-trait associations also form the basis of the new colour scheme of the dynamic GWAS diagram.
For questions and to provide feedback, please contact the GWAS team at EBI.
For bug reports and feature requests, please use our bug tracker.
Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S. and Manolio, T.A. (2009) Potential Etiologic and Functional Implications of Genome-Wide Association Loci of Human Diseases and Traits. Proc. Natl. Acad. Sci. USA. 106, 9362–9367.
Whether you have a question, would like to provide feedback on your experience using the diagram or want to make a suggestion for a new feature, please do not hesitate to contact us.
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