> 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/r2/methods/phewas/logistic-regression.md).

# Association tests

## Null models

For the null model calculation for each endpoint, we used age, sex, 10 PCs and genotyping batch as covariates.

For calculating the genetic relationship matrix, we used 49,811 independent, common, well-imputed variants with a posterior genotyping probability >0.95 and missingness <0.05 (LD r2 < 0.1, MAF > 0.05, INFO > 0.95).

[SAIGE](https://github.com/weizhouUMICH/SAIGE/) options for the null computation:&#x20;

* `LOCO = false`
* `numMarkers = 30`
* `traceCVcutoff = 0.0025`
* `ratioCVcutoff = 0.001`

## Association tests

We ran association tests against each of the 1,122 endpoints with [SAIGE](https://github.com/weizhouUMICH/SAIGE/) for each variant with a minimum allele count of 10 from the imputation pipeline (SAIGE option`minMAC = 10`). The alternative allele is always the effect allele.&#x20;

## Software

The code we used is available in [github.com/FINNGEN/SAIGE-IT/tree/master/SAIGE](https://github.com/FINNGEN/SAIGE-IT/tree/master/SAIGE). The original SAIGE codebase is available in <https://github.com/weizhouUMICH/SAIGE/>.