In this paper, we study and describe the universal Poisson deformation space of hypertoric varieties concretely. In the first application, we show that affine hypertoric varieties as conical symplectic varieties are classified by the associated regular matroids (this is a partial generalization of the result by Arbo and Proudfoot). As a corollary, we obtain a criterion when two quiver varieties whose dimension vector have all coordinates equal to one are isomorphic to each other. Then we describe all 4- and 6-dimensional affine hypertoric varieties as quiver varieties and give some examples of 8-dimensional hypertoric varieties which cannot be raised as such quiver varieties. In the second application, we compute explicitly the number of all projective crepant resolutions of some 4-dimensional hypertoric varieties by using the combinatorics of hyperplane arrangements.