GWAS

We used regenie for release 11. Regenie's main advantages are fast leave-one-chromosome-out relatedness calculation which avoids proximal contamination, and use of an approximate Firth test which gives more reliable effect size estimates for rare variants.

We used regenie version 2.2.4.

Links:

• regenie preprint

• regenie GitHub repository

• FinnGen regenie GitHub repository

• FinnGen regenie pipeline GitHub repository

We analyzed:

• ​2,447 endpoints

  • 2,444 binary endpoints

  • 3 quantitative endpoints (HEIGHT_IRN, WEIGHT_IRN, BMI_IRN)

• 453,733 samples

  • 254,618 females

  • 199,115 males

• 21,311,942 variants

We included the following covariates in the model: sex, age, 10 PCs, Finngen chip version 1 or 2 , and legacy genotyping batch.