Since the validation dataset was genotyped on a different GWAS SNP panel with a smaller number of SNPs (558183), The genotypes from our data and the data from the AGRE were imputed independently by the program IMPUTE (Marchini et al. 2007) using a phased CEU HapMap dataset as a reference (International HapMap Consortium et al. 2007). Individual genotypes with probability less than 0.90 were not included. All individuals were treated independently while doing imputation. Mendelian inconsistencies were zeroed out in PLINK (Purcell et al. 2007). The results for the imputation are found in table 1. Results on imputed SNPs missing more than 10% of the genotypes were labeled in the table 1 and should be interpreted with caution because of possible bias.
