# HLA region analysis

### HLA imputation

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 ](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 ](https://academic.oup.com/nargab/article/2/2/lqaa030/5831010)

Genotype data was constructed from the dosage data using PLINK 2. 

### Variant summary

A snp-stats report was generated with [qctool](https://www.well.ox.ac.uk/~gav/qctool_v2/) 

### GWAS

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. 

### GWAS summary

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.