In this paper, we provide an overview of statistical models for haplotype-based association studies, and summarize their features based on the design matrix. We classify the design matrix into the two types: direct and indirect. For these two kinds of matrices, we present and compare characteristics using a simple hypothetical example, and a real data set. The motivation behind this study was to provide practitioners with an improved understanding, to facilitate the informed selection of the appropriate haplotype-based model and to improve the interpretability of the models.