we expect the SNP will be present ∼50% of the time so that >50% imputation accuracy cannot be achieved for this SNP. On the other hand, knowledge of the haplotype does provide useful information about the SNP, and the rsq_hat statistic takes a value of about 0.44 in this setting. There are examples of association between imputed SNPs with similar rsq_hat statistics and complex traits that have been confirmed in follow-up genotyping (e.g. the association between CETP and HDL cholesterol) [16].
