> For the complete documentation index, see [llms.txt](https://finngen.gitbook.io/documentation/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://finngen.gitbook.io/documentation/methods.md).

# Methods

- [Participating biobanks/cohorts](https://finngen.gitbook.io/documentation/methods/cohort-description.md)
- [Genotypes](https://finngen.gitbook.io/documentation/methods/genotype-imputation.md)
- [Genotype data](https://finngen.gitbook.io/documentation/methods/genotype-imputation/genotype-data.md)
- [Genotype imputation](https://finngen.gitbook.io/documentation/methods/genotype-imputation/genotype-imputation.md)
- [SISu reference panel](https://finngen.gitbook.io/documentation/methods/genotype-imputation/sisu-reference-panel.md)
- [Software used](https://finngen.gitbook.io/documentation/methods/genotype-imputation/software-used.md)
- [LD estimation](https://finngen.gitbook.io/documentation/methods/genotype-imputation/ld-estimation.md)
- [Endpoints](https://finngen.gitbook.io/documentation/methods/endpoints.md)
- [GWAS](https://finngen.gitbook.io/documentation/methods/phewas.md)
- [Sample QC and PCA](https://finngen.gitbook.io/documentation/methods/phewas/quality-checks.md)
- [Association tests](https://finngen.gitbook.io/documentation/methods/phewas/logistic-regression.md)
- [PheWeb](https://finngen.gitbook.io/documentation/methods/pheweb.md)
- [Colocalization](https://finngen.gitbook.io/documentation/methods/colocalization.md)
- [Finemapping](https://finngen.gitbook.io/documentation/methods/finemapping.md)
- [LoF variant burden](https://finngen.gitbook.io/documentation/methods/lof-variant-burden.md): Gene-based burden test results of loss of function variants (LoFs).
- [HLA region analysis](https://finngen.gitbook.io/documentation/methods/hla-region-analysis.md)
- [Contact](https://finngen.gitbook.io/documentation/methods/contact.md)