# HLA region analysis

### HLA imputation

The HLA data was imputed from R12 genotype data, using HIBAG models created by Jarmo Ritari from the Finnish Blood Bank. More information can be found in the repository: 

[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)

### Variant summary

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

### Association testing

Association testing was performed using Regenie 2.2.4, or for some endpoints Regenie 3.3. Same settings were used as in the core GWAS analysis. See [the Association tests page](/documentation/methods/phewas/logistic-regression.md) 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.


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