Imputation was carried out using IMPUTE27 which chooses a custom reference panel for each study individual in each 2 Mb segment of the genome. We set the khap parameter of IMPUTE2 to 1000. All other parameters were set to default values. We stratified imputed variants into allele frequency bins and calculated the squared correlation between the imputed allele dosages at variants in each bin with the masked CG genotypes (called aggregate r2 in Figure 1). Non-reference allele frequency for each SNP was calculated from HRC release 1 GLs at MAC>=5 sites. Figure 1 shows the results for the Illumina Omni 1M chip. Supplementary Figures 3 and 4 show the results from the Illumina Core Exome chip and the Illumina Omni 5M chip respectively.
