# HLA association results ### Data Starting from R9, for each release, the analysis team runs association analyses for classical HLA alleles that have been imputed from the FinnGen genotype data. The imputation pipeline has been developed by Jarmo Ritari from the Finnish Blood Service. More information about the imputation is available in the [imputation pipeline repository](https://github.com/FRCBS/HLA-imputation) or in the publication: Ritari J, Hyvärinen 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, QCtools is used to generate a variant-level summary of the genotypes. ### Association analysis Association analysis of the classical HLA alleles is performed using regenie. See the core analysis documentation for more information. ### Files As of R9, the outputs of this analysis include: * A QCtool variant report * Association analysis summary statistic files * A summary of the association analysis. See the release notes for HLA analysis for more information about the data. The files are available in the green library: `/finngen/library-green/finngen_R12/finngen_R12_analysis_data/hla` Read more about [imputation of FinnGen HLA alleles](/finngen-data-specifics/green-library-data-aggregate-data/other-analyses-available/hla.md) and [data file of the imputed HLA alleles](/finngen-data-specifics/red-library-data-individual-level-data/genotype-data/types-of-genotype-files-available/imputed-hla-alleles.md). --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/hla-association-results.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.