To perform the association test with PC-based correction, we used multiple linear regression with PC1 and PC2 as covariates as implemented in the software eigenstrat12. The Armitage χ2 statistic was used to test the strength of the association. We also calculate an inflation statistic, by taking the ratio of the 50% quantile of the observed Armitage χ2 statistic with that expected under the null χ12 distribution.
