Most GWAS are built on unrelated case-control studies, e.g. studies within the Psychiatric Genomics Consortium. In this paper we investigate the difference between the odds ratio, estimated using an unrelated case-control study, and the incidence rate ratio from longitudinal designs. From simulations we see that the odds ratio is not equal to the incidence rate ratio, and that these differences are reflected in the resulting p-values. The odds ratio measures the effect of the SNP on the probability of being diseased, whereas the incidence rate ratio measures the effect on the probability of becoming diseased.