Study power depends on assumptions about the underlying disease model, in addition to effect sizes and sample sizes. When the true causative SNP is not on the genotyping chip there will typically be several SNPs on the chip which are correlated with it. One or more of these could give a signal of significant association and hence allow detection of the locus. The LD structure of the human genome is sufficiently complicated that this effect cannot be captured analytically. It must be assessed via simulation studies.
