Genotyping Quality Control & Imputation
Detailed information of genotyping data and imputation method are
described previously14. In summary, PLINK1.9 was used
to perform quality control for array data15. We
excluded SNPs with call rate < 0.98, minor allele frequency
(MAF) < 0.001, p value of Hardy–Weinberg Equilibrium (HWE) p
value < 1x10-6, and polymorphic variants.
For sample-level quality control, we excluded individuals call rate
< 0.98, heterozygosity > 5 SD, and remove
duplicate samples. Besides, the outliners from 1000 genome EAS
population (>3 IQR) were removed from the analysis. For
data after imputation, we kept variants with INFO score ≥ 0.3.