Tool Catalog

Publicly available web tools (no FinnGen account needed):

Tool	Brief summary
Risteys	Core endpoint definitions and relationships between endpoints. Results from CodeWAS and LabWAS tools and mortality from FinRegistry. Includes also Kanta lab data and their distributions.
Endpoint Browser	Tool to understand the relationships between FinnGen core endpoints
MMP	Multiple Manhattan Plot to align and browse between 2 to 20 GWAS scans
LAVAA	Lightweight Association Viewer Across Ailments to display PheWAS results for a variant as a volcano plot
OHDSI CDM Code	A site detailing the FinnGen data mapping to the OMOP common data model (CDM)
Mapping status of the Kanta lab data	Look up availability and OMOP mapping of Kanta lab tests
FinnGen github	Repository of the codes for the FinnGen analyses
PheWeb(s)	Browse publicly available GWAS results (note there are PheWebs available for multiple FinnGen releases, to access the earlier release browsers visit https://www.finngen.fi/en/access_results)
Meta-analysis Pheweb [FG-UKBB]	Browse FinnGen-UKBB GWAS meta-analysis results
Meta-analysis Pheweb [FG-MVP-UKBB]	Browse FinnGen-MVP-UKBB GWAS meta-analysis results
V3C	Variant Cluster Call Corrector

Web tools for FinnGen green data accounts:

Tool	Brief summary
FinnGen production library green	Download the accumulated FinnGen core analysis results from the Google console
PheWeb	Browse core GWAS results, conditional analysis, finemapping, colocs
User-results	Browse GWAS results for user-defined phenotypes
Coding variant browser	Additive and recessive phenotype associations for rare and common coding variants
Anno	Tool to annotate lead variants with phenotype associations, eQTLs, pQTLs and splice QTLs
Sex-diff	Endpoint GWASs separately for females/males and test for different effect sizes
Recessive GWAS	Browse core GWAS results from recessive analysis

Sandbox environment and tools for FinnGen red data accounts:

Tool	Brief summary
Sandbox	Trusted Research Environment (TRE), access to FinnGen individual level data
Atlas	OHDSI/OMOP tool to define concept sets and cohorts
Cohort Operations	Import cohorts created elsewhere and explore and operate them, e.g. by using CodeWAS and TimeCodeWAS. Launch GWAS.
LifeTrack	View the health history of an individual
TVT	Trajectory Visualization Tool to view the health trajectories of a cohort of individuals
Genotype Browser	View, edit and export genotype data
CustomGWAS	Command line tool to assist users running custom GWAS. The easiest way to launch CustomGWAS is through the Cohort Operations tool.
Pipelines	GUI to help with running Regenie, Finemapping, GATE, etc.
PGS browser	View polygenic scores for existing endpoints or a custom cohort
PheWeb users input validator	Tool for validating the format of user custom GWAS summary stats to be viewable in a PheWeb-style
Exome query tool	A command line interface allowing users to query carriers of variants in FinnGen exome data