The HLA data was constructed from dosage data provided by Jarmo Ritari from the Finnish Red Cross Blood Service. More information can be found in the repository describing the imputation:
https://github.com/FRCBS/HLA-imputation
as well as in the publication: Ritari J, Hyvä rinen K, Clancy J, FinnGen, Partanen J, Koskela S. Increasing accuracy of HLA imputation by a population-specific reference panel in a Finngen biobank cohort. NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa030, https://doi.org/10.1093/nargab/lqaa030
Genotype data was constructed from the dosage data using PLINK 2.
A snp-stats report was generated with
Association testing was performed using Regenie 2.2.4. Same settings were used as in the core GWAS analysis. See the core analysis document for more information.
A summary was created from the Regenie summary statistic outputs. This summary contains the best variant per each phenotype's summary statistic file. Pheweb links to phenotype and gene pages have been added as additional columns.