The Variant page

Another common query in the GWAS Catalog is “what other associations have been discovered for my variant of interest?”. You can search for a specific variant (typically using an rsID), gene name, or genomic region (eg 2q37.1; 6:16000000-25000000).

Searching for a variant allows you to click through to the Variant page, showing a summary of all the data in the Catalog pertaining to your variant of interest. You can see an example in the frame below (Figure 15).

Figure 15 This is an interactive subset of GWAS Catalog page to explore the variant of interest.

The Variant page has the same format as the other page types, with general variant information and links out in the Information Table at the top, followed by the Associations Table below, which summarises every association with this variant in the Catalog. The Studies Table lists every study that has reported an association with the variant.  

There are two unique features on the Variant page. Firstly, the Traits table contains a list of all the traits reported for the variant in order of frequency. This allows you to easily see the most commonly reported ones. In the example above, you can see the most commonly associated trait for this variant is platelet count, followed by other haematology traits. 

Secondly, in the Linkage disequilibrium (LD) plot tab, you can find other variants in LD with your variant of interest, within the GWAS Catalog and in Ensembl. Choose the reference population and filter by LD threshold using the options at the top of the box. Try it in the frame above. You can download all the variants in the plot using the “Download LD data” button.

Lastly, searching for a gene or genomic region in the main search page summarises all the variants annotated to that gene or genomic region on a single page. From there you can download the data or click through to each variant for more information.