Data Releases 2025
December 19th
We have released IBD Task Force modified Montreal classifications for endoscopies released earlier for IBD patients, as well as IBD Task Force time to operation & refined disease onset data.
montreal data location:
/finngen/library-red/task_force_data/IBD/Montreal_classification/
time to operation & refined disease onset data location:
/finngen/library-red/task_force_data/IBD/Refined_phenotypes/
You can read more about the data on the handbook pages for the montreal data and time to operation data.
R13 GWAS meta-analysis
3-way FinnGen + MVP + UKBB meta-analysis:
401 binary disease endpoints
46 lab measurements
3 continuous endpoints
2-way FinnGen + UKBB meta-analysis:
933 binary disease endpoints
48 lab measurements
3 continuous endpoints
gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/meta_analysis/
December 17th
We have released FinnGen KCO single-cell multiome data to Green library and to the Sandbox Red Library.
This release is based on our FinnGen multiome flagship manuscript: https://doi.org/10.1101/2025.11.25.25340489
A Handbook page describing further this data will be added soon.
A data release policy document specifically for this release is available in the FinnGen members area (https://www.finngen.fi/en/members/document/4829).
The data and documentation in Green library are available here:
gs://finngen-production-library-green/omics/singlecell/batch1_5_2025_12_15/
The data and documentation in Sandbox Red Library are available here:
/finngen/library-red/EA5/multiome/batch1_5/
According to the FinnGen Consortium Agreement, these data releases are subject to a one-year embargo and are exclusively available to FinnGen partners. FinnGen researchers who seek to use the data for publication should follow the secondary analysis procedure as described in the linked document below. Similar to other FinnGen resources, individual-level (red) data always require an analysis proposal, while summary-level (green) data require a proposal during the embargo period. Further details on the data releases and secondary analysis procedure can be found in the FinnGen members area (https://www.finngen.fi/en/members/document/4829).
December 8th
We have released FinnGen R13 Spirometry Data (version 1.0) to Sandbox.
This dataset contains harmonized spirometry measurements from 46,224 individuals across 6 Finnish biobanks, comprising 123,113 measurements. The data includes pre- and post-bronchodilator values, GLI-2012 predicted values (percent predicted, z-scores, LLN). This data is part of the FinnGen Pulmonary Task Force.
Data & documentation available in Sandbox red library:
/finngen/library-red/task_force_data/Pulmonary/Spirometry/
December 8th
We have released DF13 PGS Browser data files to Sandbox.
Detailed description of the PGS Browser is in Handbook: https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/pgs-browser
The data and documentation are available in Sandbox red library.
/finngen/library-red/finngen_R13/pgs_browser_db_1.0/
December 4th
We have released FinnGen visus data files to Sandbox.
There is data from FinnGen AMD patients from five different biobanks (Central Finland, Eastern Finland, Auria, Borealis and Tampere).
Detailed description of the OCT and visus data in Handbook is here: https://docs.finngen.fi/finngen-data-specifics/disease-specific-task-force-data/age-related-macular-degeneration-amd
The data and documentation are available in Sandbox red library.
/finngen/library-red/task_force_data/AMD/Visus/
November 13th
We have released FinnGen Rheumatology registry measurement data (version 2.0) to the Sandbox.
This is an updated version of Rheumatology register measurement data where additional calculated DAS28ESR3, DAS28ESR4, DAS28CRP3, DAS28CRP4 measurements are added, and couple of measurement variable typos are corrected ( PHYCICIAN_EVALUATED_PAIN_VAS = PHYSICIAN_EVALUATED_VAS, PHYCICIAN_EVALUATED_PAIN_VAS_CHILD = PHYSICIAN_EVALUATED_VAS_CHILD, FATIQUE = FATIGUE).
The data is further described in the Handbook: https://docs.finngen.fi/finngen-data-specifics/disease-specific-task-force-data/finnish-rheumatology-quality-register
The data and documentation are available in Sandbox red library.
/finngen/library-red/task_force_data/Rheumatic_diseases/finngen_R13_rheumatology_register_measurement_readme_2.0.txt
/finngen/library-red/task_force_data/Rheumatic_diseases/data/finngen_R13_rheumatology_register_measurement_2.0.txt.gz
November 12th
We have released FinnGen breast cancer pathology data to the Sandbox. This release is part of EA3 Oncology - Breast cancer study. Release includes data from breast cancer pathology reports. Detailed description of the EA3 breast cancer data in Handbook is here: https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-oncology-studies/ea3-study-breast-cancer-study-variables
The data and documentation are available in Sandbox red library.
/finngen/library-red/EA3_CANCER_BREAST_1.0/
October 29th
We have released DF13v3 as a separate CDM version to deliver our latest data mapping improvements while maintaining consistency with your existing searches.
What's New:
Registry Updates
Kanta lab values 2.0 data now available in the
kanta_r13_v2BigQuery table
CDM Vocabulary Updates
Updated to OMOP vocabulary August 2025 release
FinnGen endpoints now available as a separate ENDPOINT vocabulary (beta)
CDM Data Updates
Enhanced Kanta lab values 2.0 integration via MEASUREMENT_VALUE_MERGED, which includes additional values harvested and validated from other raw data sources
Exploring the Updates
You can now browse FinnGen core endpoints (e.g., "PLUM_MEDICATIO_COMORB") and view all captured concepts within the Hierarchy tab.
You can check out how we mapped and transformed FinnGen DF13 v3 data to OMOP CDM here. If you would like to raise any issues regarding the mapping and transforming DF13 data, then you can use issue section of ETL git repo.
October 24th
We have released the Finnish Rheumatic diseases Quality register medication data to red library. This is a Finnish Rheumatic diseases Quality registry medication data that has been collected from three different monitoring programs (BCB, GoTreatIt, RaiQu). Data includes information about rheumatic diseases related medication start and end dates, dosage, treatment intervals, reasons for discontinuation and adverse effects.
The data and documentation are available in Sandbox red library.
/finngen/library-red/task_force_data/Rheumatic_diseases/
October 6th
We have added 2,961 PheWAS results for proteomics and metabolomics PGSs to the PGS Browser repository: /finngen/library-red/finngen_R12/pgs_browser_db_1.0/.
In addition, 649 metabolomics scores and models have been included.
Please, note, these results are generated by Artomov lab and are made available internally within FinnGen ahead of publication, therefore we would appreciate you for following the data usage disclaimer placed in the same folder. Please, consult release notes, and meta-table for further details.
September 19th
We have released longitudinal lab value GWAS of 37 densely measured lab values. See introduction to the analyses and results in Reza Jamal’s F2F meeting presentation in Sharepoint (https://tt.eduuni.fi/sites/hy-finngen/All/_layouts/15/WopiFrame2.aspx?sourcedoc={14d16d5c-0eba-405b-8bed-a162cd91bd13}&action=edit) You can find the summary stats in the green library gs://finngen-production-library-green/lab_values/longitudinal_gwas_2025_9_17/. We also imported those into kanta.finngen.fi.
September 18th
FinnGen DF13 Finnish Red Cross Blood Service blood donor data released to Sandbox. The data and documentation are available in Sandbox red library. /finngen/library-red/finngen_R13/FRCBS_blood_donor_data/
Data description in Handbook: https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/what-phenotype-files-are-available-in-sandbox-1/other-registers/blood-donor-data-from-the-finnish-red-cross-blood-service-frcbs September 18th
FinnGen DF13 updated analysis covariates
Analysis covariates are tab-separated gzip-compressed files that contain covariate and endpoint data for each sample. These files use the recently released phenotype 3.0 data.
/finngen/library-red/finngen_R13/analysis_covariates/
Old files can still be found at:
/finngen/library-red/finngen_R13/analysis_covariates/old/
FinnGen DF13 Finnish Red Cross Blood Service blood donor data
/finngen/library-red/finngen_R13/FRCBS_blood_donor_data/
September 12th
FinnGen DF13 additional 63 endpoints
GWAS
Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/summary_stats/
Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_analysis_document_GWAS.pdf
Fine-mapping
Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/finemap/
Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_finemap.md
Autoreporting
Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/autoreporting/
Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_autoreporting.md
September 11th
FinnGen EA5 Olink Proteomics timestamps data
The file includes available timestamps and relevant information for plasma samples run during the second phase of the FinnGen project under the EA5 pilot.
/finngen/library-red/EA5/proteomics/olink/
September 2nd
We've updated OMOP CDM tables for DF13 v3 with improved mappings and enhanced functionality across our BigQuery infrastructure.
Latest Updates:
Endpoint Cohorts
Updated to August 2025 Endpoints release
Endpoint cohorts v3 BigQuery table now available
CDM Vocabulary Updates
Fixed ICD9fi code mappings
Updated ICD10fi code mappings with 400+ new combination codes
Added five FinnGen visit codes to capture drug source registry
CDM Enhancements
Kanta lab measurements now include test outcomes alongside values—filter by measurement value, test outcome, or both in Atlas
Drug exposure can now be filtered by source registry in Atlas
Updated Endpoints accessible in CO2
You can check out how we mapped and transformed FinnGen DF13 v3 data to OMOP CDM here. If you would like to raise any issues regarding the mapping and transforming DF13 data, then you can use issue section of ETL git repo.
August 19th
FinnGen DF13 phenotype data (version 3.0)
Missing endpoints were added and OMIT status of some endpoints was deliberately changed.
/finngen/library-red/finngen_R13/phenotype_3.0/
August 11th
FinnGen DF13 Chip genotypes
Data & Documentation: /finngen/library-red/finngen_R13/chipd_1.0
July 18
FinnGen R13 rheumatology register measurement data (version 1.0) released to Sandbox.
Finnish Rheumatology Quality registry that contains data about disease activity in Rheumatic disease patients. This data is part of FinnGen Rheumatic diseases Task Force.
Data & documentation:
/finngen/library-red/task_force_data/Rheumatic_diseases/
July 3
The FinnGen Twins EA5 metadata has been released to the red library. The data is available at the following location: gs://finngen-production-library-red/EA5/proteomics/second_batch/ (/finngen/library-red/EA5/proteomics/second_batch/).
The file contains the following variables, including twins zygosity, family index, and sample timestamps:
FINNGENID|Study ID
PSEUDO_FAMILY_NB|Family index number (pseudo)
APPROX_BIRTHDATE|Approximated birthdate (within +/- 15 days)
SEX|Gender (male=1, female=2)
ZYG|monozygotic=1 and dizygotic=2
AGE|Age at visit/sample
WEIGHT1|Weight (kg)
HEIGHT|Height (cm)
WAIST|Waist circumference (cm)
APPROX_DATE1|Approximated visit/sample date (within +/- 15 days)
Detailed description of the EA5 Twins Olink proteomics data (i.e., Batch 2.2 Twins), can be found in Handbook here: https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/omics-data/proteomics/expansion-area-5-proteomics-data
July 2
FinnGen R13 vaccination register data (version 1.0) released to Sandbox at gs://finngen-production-library-red/finngen_R13/vaccination_register_1.0/.
July 2
Release of update of the kanta data. This release does not contain new lab/samples but does contain one new column and contains fixes to issues we've been collecting during the months since the first release. Files can be found at gs://finngen-production-library-red/finngen_R13/kanta_lab_2.0/ Here's a summary of the changes:
Here is a list of all the technical changes covered in the Omop mapping -
We addressed issues in conversion of a certain non multiplicative unit for OMOP ID 3004410 (Mass fraction %-->mmol/mol 10.93*X-23.50 )
We added a new column: TEST_OUTCOME_TEXT_EXTRACTED. It contains abnormality texts extracted from free text after standardization. It's formatted as [<\>]|[VALUE]|[UNIT?]
Also, the file and folder structure have been simplified. There is only one folder and the main file finngen_R13_kanta_lab_2.0[.txt.gz|.parquet] contains the most useful columns for analysis, while the other file finngen_R13_kanta_lab_2.0_extended_columns contains metadata columns (e.g. reference ranges) that are mostly empty along with some source column (e.g. source test name, source values/units) for debugging purposes. The files are connected by a ROW_ID column that is unique to each entry across the two files.
Please take a look at the handbook page for a general overview of the data and at the github page or technical details.
July 1
FinnGen DF13 Colocalization data
Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/colocalization/
Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_colocalization.md
June 30
FinnGen DF13 genetic correlation and conditional analysis results:
Data genetic correlations: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/genetic_correlation/
Data conditional analysis: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/conditional_analysis/
June 19
FinnGen DF13 HLA association analysis results
Data: /finngen/library-green/finngen_R13/finngen_R13_analysis_data/hla/
Documentation: /finngen/library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_hla_analysis.pdf
June 19
Updated OMOP CDM tables for DF13 and other BigQuey tables. The details are as follows Latest updates
Birth and Kidney registries
There is no official release of birth and kidney registries for DF13
We filtered out DF13 samples from DF12 birth and kidney registries data and released for DF13
Endpoint cohorts v2
Updated to Endpoints of May 2025 release
You can check the BigQuery table "finngen-production-library.sandbox_tools_r13.endpoint_cohorts_r13_v2"
You can check out how we mapped and transformed FinnGen DF13 data to OMOP CDM here.If you would like to raise any issues regarding the mapping and transforming DF13 data, then you can use issue section of ETL git repo.
June 10
FinnGen DF13 imputed HLA genotypes
Data: /finngen/library-red/finngen_R13/hla_1.0/
Documentation: /finngen/library-red/finngen_R13/hla_1.0/finngen_R13_hla_data.pdf
June 10
The TWINGEN EA6 phenotype data has been released to the red library.
You can find the data in the following path: /finngen/library-red/EA6_TWINGEN/data/ The data contains telephone-based cognitive screening, blood-based biomarkers of Alzheimer’s disease and related dementias, health and lifestyle questionnaires, accelerometer-based physical activity measurement, computerized cognitive assessment, in-person neuropsychological testing and Oura ring-based sleep and physical activity measurement (listed in a decreasing order of the amount of data available). See Vuoksimaa, Saari et al. (2024) for more information about the procedures and data collection.
Detailed readme files are available in the red library: /finngen/library-red/EA6_TWINGEN/
June 3
FinnGen phenotype data has been updated to 2.0, at /finngen/library-red/finngen_R13/phenotype_2.0. Some new endpoints were added, and some old ones were modified.
May 31
FinnGen DF13 GWAS
Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/summary_stats/
Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_analysis_document_GWAS.pdf
FinnGen DF13 Fine-mapping
Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/finemap/
Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_finemap.md
FinnGen DF13 Autoreporting
Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/autoreporting/
Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_autoreporting.md
May 7
THL Super Olink Proteomics data
This is a small plasma proteomics dataset (with Olink Explore HT, ~5.3K proteins) from (n=92) SUPER study participants. The SUPER study focuses on the progression of psychotic disorders, and the individuals for whom we analyzed their proteomics were selected because they are carrying certain rare variants associated with psychotic disorders. For additional information on this dataset, please contact Olli Pietiläinen ([email protected]).
/finngen/library-red/omics/proteomics/THL_SUPER/
April 22
FinnGen DF13 truncated endpoint file
/finngen/library-red/finngen_R13/truncated_endpoint_file_1.0/
FinnGen DF13 parental data
/finngen/library-red/finngen_R13/parental_causes_of_death_1.0/
/finngen/library-red/finngen_R13/parental_endpoint_1.0/
April 10
FinnGen DF13 analysis covariates Analysis covariates are tab-separated gzip-compressed files that contain covariate and endpoint data for each sample.
/finngen/library-red/finngen_R13/analysis_covariates/
FinnGen DF13 GRM data GRM contains a high-quality LD-pruned subset of the imputed genotypes in Plink bed-format.
/finngen/library-red/finngen_R13/grm_1.0/
FinnGen DF12 OMICSPRED PGS models released to Sandbox.
FinnGen PGS Browser Data Release R12 Notes Note: The current release only includes proteomics models from OmicsPred. All data are derived from OmicsPred, based on three datasets: UKBB (EUR), n=2,312 INTERVAL, n=273 Somalogic, n=1,645
More information in the provided readme
/finngen/library-red/finngen_R12/pgs_browser_db_1.0/
April 8
DF13 cancer screening data (breast and cervical)
/finngen/library-red/finngen_R13/cancer_screening_1.0/
April 4
DF13 detailed cancer data
/finngen/library-red/finngen_R13/cancer_detailed_1.0/
DF13 Extended Hilmo and Avohilmo data
/finngen/library-red/finngen_R13/hilmo_avohilmo_extended_1.0/
April 3
Variant-wise QC metrics files and index files for the FinnGen imputation reference panel. The release includes variant-wise QC metrics TSV files for the Sisu v4.2 reference panel, reflecting different QC stages:
Raw data
Post sample-wise QC
Post sample-, genotype-, and variant-wise QC
Genotype- and variant-wise QC step removed variant lists, including extra column [failed_filter].
This column gives the reason why this variant has been filtered out during genotype- and variant-wise QC step.
Data: gs://finngen-production-library-green/imputation_panel/v4.2/variant_qc/sisu4.2_panel_var_wise_QC_metrics/
March 22
Genotype bgen/plink
/finngen/library-red/finngen_R13/plink_1.0/
/finngen/library-red/finngen_R13/bgen_1.0/
PCA: /finngen/library-red/finngen_R13/pca_1.0/
PCA inliers (unrelated finns) : 281515
PCA outliers (related finns) : 218975
PCA rejected (non finns and duplicates) : 19482
PCA final samples : 500490
KINSHIP: /finngen/library-red/finngen_R13/kinship_1.0/
March 21
R13 visual impairment register data
/finngen/library-red/finngen_R13/visual_impairment_register_1.0/
March 21
We have updated OMOP CDM tables for DF13 with new registry data and vocabulary updates. Latest updates
Drug Events
Outer join of Kela reimbursement, Kanta prescription and Kanta medication delivery registries
Readme file contains details of the columns
Updated vocabularies
You can check out how we mapped and transformed FinnGen DF13 data to OMOP CDM here. If you would like to raise any issues regarding the mapping and transforming DF13 data, then you can use issue section of ETL git repo.
March 20
R13 Kanta lab & analysis data: /finngen/library-red/finngen_R13/kanta_lab_1.0/ /finngen/library-red/finngen_R13/kanta_analysis_1.0/ March 17
FinnGen R13 service sector data(version 1.0) released to Sandbox .
/finngen/library-red/finngen_R13/service_sector_data_1.0/
March 10
Kanta lab value analysis v2 of 388 labs. Main changes are that all lab values are now inverse rank normalised to make comparisons/meta-analyses easier. Additionally certain derived lab values are also analysed (e.g. non-HDL cholesterol, EGFR computed from creatinine). N samples for many binary tests(mostly antibody tests) is increased by not only using result text (positive/abnormal/high) but including manually curated thresholding of lab values. Find below description of the analyses and metadata of all lab values analysed. Browser at kanta.finngen.fi is updated to display these new results. Find flat files of the results in green library gs://finngen-production-library-green/lab_values/gwas_release_2025_3_10/
Find the lab value phenotype file used in the analysis in red library (library-red/finngen_R12/analysis_covariates/kanta_lab_v2analysis_data_2025_3_10.txt.gz)
5 March
FinnGen DF13 genotypes and phenotypes released to Sandbox red library.
The current data statistics are: Number of individuals with genotypes = 519,972 Number of individuals with endpoints = 519,972 Number of imputed variants = 21,331,644 Number of endpoints = 4,662
You can find the data and documentation in Sandbox red library:
Genotypes in VCF format & Documentation: /finngen/library-red/finngen_R13/genotype_1.0/
Phenotypes & Documentation: /finngen/library-red/finngen_R13/phenotype_1.0/
The lower number of individuals in this release compared to release 12 is due to excluding new sample denials. However, the registry data is updated from R12 for all individuals.
28th February
FinnGen 3 QCd Olink proteomics dataset of 2094 individuals.
protein expression data:
library-red/omics/proteomics/olink_genewiz_batch1_QCd_2025_28_02/
pQTL and finemap in 1,829 independent samples of the above:
gs://finngen-production-library-green/omics/proteomics/olink_genewiz_batch1_QCd_2025_28_02/
13 February
FinnGen EA5 PBMC metadata files released to Sandbox. This file includes timestamp information for all PBMC samples FRC Blood Service Biobank has delivered to FinnGen between 2021-2024. More information is available in the provided readme.
/finngen/library-red/ EA5/omics_metadata/20250130_EA5_PBMCs_Metadata_All.csv
/finngen/library-red/ EA5/omics_metadata/20250204_EA5_PBMC_Metadata_Readme.md
5 February
FinnGen EA5 plasma metadata files released to Sandbox. This file includes timestamp information for all plasma samples FRC Blood Service Biobank has delivered to FinnGen between 2021-2024. More information is available in the provided readme.
/finngen/library-red/ EA5/omics_metadata/20250204_EA5_Plasma_Metadata_All.csv
/finngen/library-red/EA5/omics_metadata/20250204_EA5_Plasma_Metadata_Readme.md
9 January
FinnGen EA3 endometriosis data was supplemented by pain related text mining data, ICD-10 data and Nordic classification of surgical procedures (NCSP) data. ICD-10 and NCSP codes have been used for selecting cohort for endometriosis related pain. EA3 endometriosis medication data was released to Sandbox earlier.
/finngen/library-red/EA3_WOMENS_HEALTH_ENDOMETRIOSIS_1.0/
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