Summary data based fine-mapping methods assume that the causal variants are included in the data. Recent advances in z-score imputation (Lee et al., 2013; Pasaniuc et al., 2014) help to satisfy this requirement also when a causal variant might not be genotyped. However, some SNPs are difficult to impute because they are not tagged well by the SNPs in the data. We do not expect to capture well the association signal from such SNPs either through imputation or indirectly through other SNPs in the data.
