The HLA data was imputed from R11 genotype data, using HIBAG models created by Jarmo Ritari from the Finnish Blood Bank. More information can be found in the repository:
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,
Genotype data was constructed from the dosage data using PLINK 2.
Variant summary
A snp-stats report was generated with
Association testing
Association testing was performed using Regenie 2.2.4. Same settings were used as in the core GWAS analysis. See for more information.
Association summary
A summary was created from the regenie summary statistic outputs. This summary contains the most significant variant (by p-value) for each phenotype. Pheweb links to phenotype and gene pages have been added as additional columns.