The PheWAS tool lets you explore phenome-wide association results for a specific genetic variant across multiple traits, disease panels, cohorts, and selected studies.
Use it to identify whether a variant is associated with one phenotype or with a broader range of health-related traits.
Before you begin
Select at least one study before plotting a PheWAS result.
[Screenshot 1: Use the full PheWAS page. Add red boxes around “Add Studies” and “Load from Group”.]
- Select Add Studies to choose individual studies.
- Select Load from Group to use a predefined group of studies.
- The selected studies will be included when the PheWAS is plotted.
Select panels to include
Use Panels to include to choose the phenotype panels you want to analyse. This is a required field.
[Screenshot 2: Red box around the “Panels to include” dropdown.]
Panels determine the phenotypes and outcome categories included in your PheWAS plot.
Refine the scope of your analysis
You can optionally narrow the results using the additional filters.
[Screenshot 3: Red boxes around “Panels to exclude”, “Cohorts”, and “Study Population”.]
- Panels to exclude — Remove selected phenotype panels from the analysis.
- Cohorts — Restrict the analysis to one or more available cohorts.
- Study Population — Restrict results to a specific study population, where available.
Leave these fields blank if you want to include all available data within your selected panels and studies.
Enter a genetic variant
Enter the variant you want to investigate in the Variant field.
[Screenshot 4: Red box around the Variant field, showing the example 19:49659652:C:G.]
You can enter a variant using either of the following formats:
- Chromosome, position, other allele, and effect allele
Example:19:49659652:C:G - rsID
Example:rs429358
Ensure that the chromosome, genomic position, and alleles match the reference data used in the selected studies.
Plot the PheWAS results
After selecting panels and entering a variant, select Plot PheWAS.
[Screenshot 5: Red box and arrow pointing to the “Plot PheWAS” button.]
The portal will generate a visual summary of associations between the selected variant and the included phenotypes.
Interpreting results
The resulting PheWAS plot provides an overview of the phenotypes associated with your selected variant across the chosen panels, studies, and filters.
Use the plot to:
- Identify phenotypes with notable association signals.
- Compare associations across disease or trait categories.
- Explore potential pleiotropic effects of a variant.
- Prioritise findings for further investigation.
Tips
- Begin with broad panel selection, then use exclusions or cohort filters to focus your analysis.
- Confirm that the variant is entered in a supported format before plotting.
- If no results are displayed, check the selected studies, panels, variant format, and available study population.