# Tool Catalog

### Publicly available web tools (no FinnGen account needed):

<table><thead><tr><th width="207">Tool</th><th width="456">Brief summary</th><th data-hidden>Location</th></tr></thead><tbody><tr><td><a href="https://risteys.finregistry.fi/">Risteys</a></td><td>Core endpoint definitions and relationships between endpoints. Results from CodeWAS and LabWAS tools and mortality from <a href="https://www.finregistry.fi/">FinRegistry</a>. Includes also Kanta lab data and their distributions.</td><td><a href="https://risteys.finregistry.fi/">https://risteys.finregistry.fi/</a></td></tr><tr><td><a href="https://geneviz.aalto.fi/EB_testing/?view=lists">Endpoint Browser</a></td><td>Tool to understand the relationships between FinnGen core endpoints</td><td><a href="https://geneviz.aalto.fi/EB_testing/?view=lists">https://geneviz.aalto.fi/EB_testing/?view=lists</a> (under development)</td></tr><tr><td><a href="https://mmp.finngen.fi/">MMP</a></td><td>Multiple Manhattan Plot to align and browse between multiple GWAS scans, including the publicly available core GWAS results.</td><td><a href="https://geneviz.aalto.fi/MMP/dashboard/">https://geneviz.aalto.fi/MMP/dashboard/</a></td></tr><tr><td><a href="https://geneviz.aalto.fi/LAVAA/">LAVAA</a></td><td>Lightweight Association Viewer Across Ailments to display PheWAS results for a variant as a volcano plot</td><td><a href="https://geneviz.aalto.fi/LAVAA/">https://geneviz.aalto.fi/LAVAA/</a></td></tr><tr><td><a href="https://finngen.github.io/ETL/">OHDSI CDM Code</a></td><td>A site detailing the FinnGen data mapping to the OMOP common data model (CDM)</td><td>?</td></tr><tr><td><a href="https://finngen.github.io/kanta_lab_harmonisation_public/">Mapping status of the Kanta lab data</a></td><td>Look up availability and OMOP mapping of Kanta lab tests</td><td></td></tr><tr><td><a href="https://github.com/FINNGEN/">FinnGen github</a></td><td>Repository of the codes for the FinnGen analyses</td><td></td></tr><tr><td><a href="https://r12.finngen.fi/">PheWeb</a> (public)</td><td>Browse publicly available GWAS results (note there are PheWebs available for multiple FinnGen releases, to access the earlier release browsers visit <a href="https://www.finngen.fi/en/access_results">https://www.finngen.fi/en/access_results</a>)</td><td></td></tr><tr><td><a href="https://metaresults-ukbb.finngen.fi">Meta-analysis Pheweb</a> [FG-UKBB]</td><td>Browse FinnGen-UKBB GWAS meta-analysis results</td><td></td></tr><tr><td><a href="https://mvp-ukbb.finngen.fi/">Meta-analysis Pheweb </a>[FG-MVP-UKBB]</td><td>Browse FinnGen-MVP-UKBB GWAS meta-analysis results</td><td></td></tr><tr><td><a href="https://infodesign.aalto.fi/projects/v3c-variant-cluster-call-corrector/">V3C</a></td><td>Variant Cluster Call Corrector</td><td></td></tr><tr><td><a href="https://annopublic.finngen.fi/">Anno</a> (public)</td><td>Tool to annotate lead variants with phenotype associations, eQTLs, pQTLs and splice QTLs</td><td></td></tr><tr><td><a href="https://tools.risteys.finngen.fi/definition-checker/">Endpoint Definition Checker</a></td><td>Checks several rules to validate an Endpoint Definition file</td><td></td></tr></tbody></table>

### Web tools for FinnGen green data accounts:

<table><thead><tr><th width="207">Tool</th><th width="454">Brief summary</th><th data-hidden>Location</th></tr></thead><tbody><tr><td><a href="https://console.cloud.google.com/storage/browser/finngen-production-library-green">FinnGen production library green</a></td><td>Download the accumulated FinnGen core analysis results from the Google console</td><td></td></tr><tr><td><a href="https://results.finngen.fi">PheWeb</a></td><td>Browse core GWAS results, conditional analysis, finemapping, colocs</td><td><a href="https://results.finngen.fi/">results.finngen.fi</a></td></tr><tr><td><a href="https://userresults.finngen.fi/">User-results</a></td><td>Browse GWAS results for user-defined phenotypes</td><td><a href="https://userresults.finngen.fi/">https://userresults.finngen.fi/</a></td></tr><tr><td><a href="https://results.finngen.fi/coding">Coding variant browser</a></td><td>Additive and recessive phenotype associations for rare and common coding variants</td><td><a href="https://results.finngen.fi/coding">https://results.finngen.fi/coding</a></td></tr><tr><td><a href="https://anno.finngen.fi/">Anno</a></td><td>Tool to annotate lead variants with phenotype associations, eQTLs, pQTLs and splice QTLs</td><td><a href="https://anno.finngen.fi/">https://anno.finngen.fi/</a></td></tr><tr><td><a href="https://sex-diff.finngen.fi/">Sex-diff</a></td><td>Endpoint GWASs separately for females/males and test for different effect sizes</td><td></td></tr><tr><td><a href="https://recessive.finngen.fi/">Recessive GWAS</a></td><td>Browse core GWAS results from recessive analysis</td><td></td></tr><tr><td><a href="https://drugs.finngen.fi/">Drugs GWAS</a></td><td>PheWeb for ATC-based phenotypes</td><td></td></tr><tr><td><a href="https://kanta.finngen.fi/">Kanta lab values GWAS</a></td><td>PheWeb for Kanta lab values</td><td></td></tr><tr><td><a href="https://finngenie.fi/">Finngenie</a></td><td>Explore and interpret human genetics results, phenotypes, genes, variants, biological interpretations, and more. Powered by Claude Sonnet 4.6 with direct access to a rich genetics datasets.</td><td></td></tr><tr><td><a href="https://metaresults-aou.finngen.fi/">https://metaresults-aou.finngen.fi/</a> [FG-AoU]</td><td>Browse FinnGen-AllofUs GWAS meta-analysis results</td><td></td></tr><tr><td><a href="https://results.taskforce.finngen.fi/">Disease specific task force PheWeb</a></td><td>PheWeb for browsing FinnGen 3 Disease Specific Task Force GWAS results</td><td></td></tr></tbody></table>

### Sandbox environment and tools for FinnGen red data accounts:

<table><thead><tr><th width="165.6666259765625">Tool</th><th width="460">Brief summary</th><th data-hidden>Location</th></tr></thead><tbody><tr><td><a href="https://sandbox.finngen.fi/login">Sandbox</a></td><td>Trusted Research Environment (TRE), access to FinnGen individual level data</td><td></td></tr><tr><td><a href="/pages/1pOSy0ISLJhNrtUriuhC">Atlas</a></td><td>OHDSI/OMOP tool to define concept sets and cohorts</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/VJYHlLSbUjeMYUVGY6PW">Cohort Operations</a></td><td>Import cohorts created elsewhere and explore and operate them, e.g. by using CodeWAS and TimeCodeWAS. Launch GWAS.</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/MlNIN4Dc16VLYpVdGhkS">LifeTrack</a></td><td>View the health history of an individual</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/DSg4NPXZEttfIKSxCv35">TVT</a></td><td>Trajectory Visualization Tool to view the health trajectories of a cohort of individuals</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/-MhYMPpqX6n8m06KcS9G">Genotype Browser</a></td><td>View, edit and export genotype data</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/-MhYMPplWKV2Cmn_OXvw">CustomGWAS</a></td><td>Command line tool to assist users running custom GWAS. The easiest way to launch CustomGWAS is through the <a href="/pages/VJYHlLSbUjeMYUVGY6PW">Cohort Operations</a> tool.</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/-MhYMPpoebI2O6qewHX2">Pipelines</a></td><td>GUI to help with running Regenie, Finemapping, GATE, etc.</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/yFV64RowgF2kAJg5vAyZ">PGS browser</a></td><td>View polygenic scores for existing endpoints or a custom cohort</td><td>Applications>FinnGen</td></tr><tr><td><a href="/pages/nU8dEfYma22Rz1NGjqpy">PheWeb users input validator</a></td><td>Tool for validating the format of user <a href="https://finngen.gitbook.io/finngen-handbook/working-in-the-sandbox/which-tools-are-available/untitled">custom GWAS</a> summary stats to be <a href="https://finngen.gitbook.io/finngen-handbook/working-in-the-sandbox/which-tools-are-available/untitled/how-to-set-up-a-pheweb-browser-for-summary-statistics">viewable in a PheWeb-style</a></td><td></td></tr><tr><td><a href="/pages/SHkw2yZYjQjXWIyRQIrB">Exome query tool</a></td><td>A command line interface allowing users to query carriers of variants in FinnGen exome data</td><td></td></tr><tr><td><a href="https://mmp.finngen.fi/">MMP</a></td><td>Multiple Manhattan Plot to align and browse between multiple GWAS scans. With finngen.fi account option to compare also results from userresults.fi and core GWAS results from the latest data freeze.</td><td></td></tr><tr><td>EHR browser</td><td>Tool for browsing FinnGen OMOP data</td><td></td></tr></tbody></table>


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