Relation Gelfand-Tsetlin $\mathfrak{gl}_n$-modules were introduced in [FRZ19], and are determined by some special directed graphs and Gelfand-Tsetlin characters. In this work we constructed polyhedra associated with the class of relation modules, which includes as a particular case, any classical Gelfand-Tsetlin polytope. Following the ideas presented in [LM04] we give a characterization of $d$-faces of the associated polyhedra in terms of a matrix related to the corresponding graph.