[i] Quality measures for the imputation of the Health 2000 data set with HapMap2 (HM2), smaller HapMap3 reference of 81 individuals selected randomly from the HapMap3 CEU samples (HM3-s), HapMap3 (HM3), Finnish HapMap3 (FIN), and the combined HapMap3 (FIN + HM3) references. R² is the square of the linear correlation between imputed allele dosage and genotyped SNP and R²MACH is the quality measure from MACH calculated as the square of the linear correlation between the predicted haplotypes. The median proportion of SNPs in concordance is calculated using genotyped and imputed best-guess genotypes. This is the median proportion of genotypes that are concordant with the best-guess imputations, taken across all imputed SNPs on chromosome 21.

[ii] ^aThe common SNPs having MAF ≥ 0.05.

[iii] ^bSNPs having MAF < 0.05 in Health 2000 genotyped data.