PheWeb
Last updated
Last updated
The PheWeb portal can be used to browse results from FinnGen's predetermined endpoints (or 'phenotypes') a.k.a. core analysis results. FinnGen PheWeb tutorial is available here.
These clinician curated endpoints were analysed for genetic associations, which allows for disproportionate case-control numbers and corrects for relatedness between samples with a sparse genetic relatedness matrix.
The results from each association run are uploaded onto the PheWeb portal, which can be accessed by clicking this link:
Home Page
The figure below shows the a table of the first few endpoints ('phenotypes') in FinnGen with the highest numbers of GWAS significant loci, along with the summary of case-control analyses and the number of hits.
You can reorder the table by clicking on the appropriate header value (in the figure above, we clicked on GWAS significant loci to order the table based on the number of GWAS loci).
From home page in PheWeb, you can also go directly to coding variant browser by clicking the icon 'Coding' in the top right corner.
Endpoint Page
Upon clicking an endpoint ('phenotype'), you will then be directed to the endpoint's page which will contain information such as case-control numbers and results from the association scan of the endpoint. In the following screenshot, we show the endpoint results for “Type 2 diabetes, wide definition”.
On the endpoint page, you will find a similar Manhattan plot from the association scan which summarizes the association results for your endpoint.
Scrolling further, you will also be able to see the Manhattan plot in a tabular format, distinguished by either the traditional GWAS hits or based on a credible set.
Variant Page
You can also browse based on a variant of your choice and see a PheWas plot:
The variant page shows the information on the gene that the variant is in, the most severe consequence annotation of the variant (from VEP), its allele frequency, whether the variant was imputed or not (INFO score), and links to external sites to obtain further information on the variant such as gnomAD, the UCSC genome browser, and the GWAS catalog.
The Manhattan plot shown in the figure above also shows p-values from the association scans for FinnGen endpoints. Scrolling down, you will again be able to see the association scan results for the FinnGen endpoints in this variant in a tabular format.
To see the corresponding LAVAA plot, you can click show lavaa plot on top of the manhattan plot.
All results (endpoint and variant-wise) can be downloaded in a tabular format by clicking Download table.
Gene Page
Gene pQTL and disease colocalizations
The gene page of the FinnGen PheWeb browser can be found from https://r12.finngen.fi/gene/<gene> by specifying the gene symbol of interest. The bottom section of the page contains gene pQTL and disease colocalization data available for the FinnGen imputed SNPs. The main table contains summary of credible sets gathered from Susie finemapping results and combined across Olink and Somascan proteomics QTL platforms (FinnGen and UK Biobank Pharma Proteomics Project). The main table includes the following columns:
source - pQTL platform source (i.e. FinnGen Olink, FinnGen Somascan, UKB-PPP)
region - region for which the fine-mapping was run
CS - running number for independent credible sets in a region
variant - top variant associated with the credible set
CS bayes factor (log10)
CS min r2 - minimum R2 correlation between variants in the credible set
beta - top variant effect size
p-value - top variant p-value
CS PIP - overall Posterior Inclusion Probability (PIP) of the variant
consequence - most severe consequence of the variant
gene most severe - gene corresponding to most severe consequence of the variant
The nested sub-table for a single gene pQTL contains a list of disease colocalizations between the FinnGen endpoints and the pQTL in question colocalizing with the lead variant of the pQTL (read more about colocalizations in FinnGen). The sub-table includes the following columns:
phenotype - FinnGen endpoint (by clicking to the phenotype you will be navigated to the PheWeb region page corresponding to the phenotype in question)
description - FinnGen endpoint description
clpp - causal posterior probability calculated for a colocalization
clpa - causal posterior agreement calculated for a colocalization
len intersect - CS intersect
len cs1 - FinnGen endpoint credible set size
len cs2 - pQTL credible set size
All results can be downloaded in a tabular format by clicking Download table.
Note: PheWeb is continuously being developed, and some features available in newer DFs may not be available in PheWeb versions for earlier DFs.
