An additional check of the imputation accuracy was performed; 10% of the SNPs were randomly masked, and correctness of imputation was determined by comparing imputed genotypes with the masked ones. More than 99% of masked SNPs passed the default imputation threshold of r2=0.3, so that our data passed this additional QC. For validation of the GWAS results, the 89 top-ranking SNPs were re-genotyped with the Sequenom MassArray platform. Here, we compare imputed and measured genotypes of these top-ranking SNPs.
