# 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:

[https://r6.finngen.fi/](https://r6.finngen.fi/)

**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.

![](https://finngen.gitbook.io/~gitbook/image?url=https%3A%2F%2F3072695768-files.gitbook.io%2F%7E%2Ffiles%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252F-MhYL0UTLjqsuIdK0SSO%252Fuploads%252Fgit-blob-db991dc2659e6173e79549cf690b43bdcef108bf%252Fpheweb1.png%3Falt%3Dmedia\&width=768\&dpr=4\&quality=100\&sign=64e0fb88\&sv=2)

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_”.

![](https://finngen.gitbook.io/~gitbook/image?url=https%3A%2F%2F3072695768-files.gitbook.io%2F%7E%2Ffiles%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252F-MhYL0UTLjqsuIdK0SSO%252Fuploads%252Fgit-blob-9e17bf3a276fb8c6ef8a72662d4b1642f617b56b%252Fpheweb2.png%3Falt%3Dmedia\&width=768\&dpr=4\&quality=100\&sign=3308446f\&sv=2)

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).

![](https://finngen.gitbook.io/~gitbook/image?url=https%3A%2F%2F3072695768-files.gitbook.io%2F%7E%2Ffiles%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252F-MhYL0UTLjqsuIdK0SSO%252Fuploads%252Fgit-blob-3737ebc547165a96078fd31a66f6e83102e55b95%252Fpheweb3.png%3Falt%3Dmedia\&width=768\&dpr=4\&quality=100\&sign=6c9f7443\&sv=2)

**Variant Page**

You can also browse based on a variant of your choice and see a PheWas plot:

![](https://finngen.gitbook.io/~gitbook/image?url=https%3A%2F%2F3072695768-files.gitbook.io%2F%7E%2Ffiles%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252F-MhYL0UTLjqsuIdK0SSO%252Fuploads%252Fgit-blob-42939585cf14373ee4b2ff96bb911f95f155e68e%252FPheWeb_variantPage.jpg%3Falt%3Dmedia\&width=768\&dpr=4\&quality=100\&sign=89c8b96e\&sv=2)

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**

![](https://finngen.gitbook.io/~gitbook/image?url=https%3A%2F%2F3072695768-files.gitbook.io%2F%7E%2Ffiles%2Fv0%2Fb%2Fgitbook-x-prod.appspot.com%2Fo%2Fspaces%252F-MhYL0UTLjqsuIdK0SSO%252Fuploads%252FQwWW7q9Ym41fL9KwNPNx%252FScreenshot%25202023-10-18%2520at%252013.45.52.png%3Falt%3Dmedia%26token%3Dcd4fd2d3-4c3f-48a3-ae94-04dece571c84\&width=768\&dpr=4\&quality=100\&sign=3c0df1e8\&sv=2)

The gene page of the FinnGen PheWeb browser can be found from [https://r12.finngen.fi/gene/\<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](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`.

<mark style="background-color:yellow;">**Note:**</mark> <mark style="background-color:yellow;"></mark><mark style="background-color:yellow;">PheWeb is continuously being developed, and some features available in newer DFs may not be available in PheWeb versions for earlier DFs.</mark>
