- Course overview
- Search within this course
- What is the GWAS Catalog?
- How to access and navigate the GWAS Catalog
- Summary Statistics
- How to get data from the GWAS Catalog
- Summary
- Try it for yourself
- Quiz: Check your learning
- Your feedback
- Get help and support on the GWAS Catalog
- References
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The Study page
Where a publication contains more than one GWAS, each separate GWAS is included as a separate Study. Using the example from the previous page, you can see this publication contains 6 studies of different blood pressure traits. To find detailed information on each study, you can click through from the Study table to each individual Study entry.
Try it in the frame below (Figure 11) – click on the “Studies” button, and then click on a study accession (e.g. GCST007095) to access the Study page.
Figure 11 This is an interactive subset of GWAS Catalog page to explore the studies associated to the publication.
On the Study page, in the Information Table, you will find details of the samples used, genotyping method and number of SNPs analysed, and the trait under study. You can find more information on how we describe the samples in our recent publication (4). From this table you can also access full summary statistics for the study (where available).
Scroll down to find the list of Associations from this study. Each Associations table contains the following information:
- SNP – The variant most strongly associated with the trait, reported as the rsID, along with the risk/effect allele. The association may also be with a haplotype or SNPxSNP interaction. The button links out to the Ensembl page with further details about the variant.
- RAF – Risk allele frequency – the proportion of the sampled control population carrying the trait-associated variant
- p-value – The probability that the variant is associated with the trait that is listed
- OR – Odds ratio – the number of times someone is more likely to exhibit the disease/trait if they possess the risk/effect allele
- Beta – Regression coefficient to indicate the effect size on the trait of possessing the risk/effect allele
- Cl – The 95% confidence interval for the odds ratio or beta (depending on which is reported)
- Mapped genes – The gene that the variant is mapped within, or the closest upstream and downstream genes, according to Ensembl
- Reported trait – A description of the trait examined in the study based on language reported in the publication
- Study accession – Identifier of the Study the association was discovered in
This table is linked to the variant, gene and trait pages, which we will explore in more detail in the next section.