To download FinnGen summary statistics you will need to fill the online form at this link. You will then receive an email containing the detailed instructions for downloading the data.
Please remember to acknowledge the FinnGen study when using these results in publications.
You can use the following text:
We want to acknowledge the participants and investigators of FinnGen study.
The Manifest file with the link to all the downloadable summary statistics is available at: https://storage.googleapis.com/finngen-public-data-r2/summary_stats/r2_manifest.tsv
GWAS summary stats (tab-delimited, bgzipped, genome build 38, filtered to INFO > 0.6, tabix index files included) are named as {endpoint}.gz. For example, endpoint I9_CHD has I9_CHD.gz and I9_CHD.gz.tbi.
To learn more about the methods used, see section GWAS.
The {endpoint}.gz have the following structure:
Column name
Description
chrom
chromosome on build GRCh38 (1-22, X)
pos
position in base pairs on build GRCh38
ref
reference allele
alt
alternative allele (effect allele)
rsids
variant identifier
nearest_genes
nearest gene name from variant
pval
p-value from SAIGE
beta
effect size estimated with SAIGE for the alternative allele
sebeta
standard deviation of effect size estimated with SAIGE
maf
minor allele frequency
maf_cases
minor allele frequency among cases
maf_controls
minor allele frequency among controls