# PheWeb
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](https://vimeo.com/user18033117).
These [clinician curated endpoints](https://www.finngen.fi/en/researchers/clinical-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](https://r12.finngen.fi/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**](https://finngen.gitbook.io/documentation/methods/finemapping).
**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](https://www.ensembl.org/info/docs/tools/vep/index.html)), 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](https://gnomad.broadinstitute.org/), the [UCSC genome browser](https://genome.ucsc.edu/), and the [GWAS catalog.](https://www.ebi.ac.uk/gwas/)
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](https://pubmed.ncbi.nlm.nih.gov/36908397/), 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/\](https://r12.finngen.fi/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 ](https://finngen.gitbook.io/documentation/methods/finemapping)gathered from [Susie ](https://stephenslab.github.io/susieR/)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](https://finngen.gitbook.io/documentation/r7/methods/colocalization)). 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`.
**PheWeb for previous data releases**
The PheWeb pages for previous data releases are available at
DF6:
**Note:** PheWeb is continuously being developed, and some features available in newer DFs may not be available in PheWeb versions for earlier DFs.