We present a molecular modeling study analyzing nanometer-scale strain variations in graphene as a function of externally applied tensile strain. We consider two different mechanisms that could underlie nanometer-scale strain variations: static perturbations from lattice imperfections of an underlying substrate and thermal fluctuations. For both cases we observe a decrease in the out-of-plane atomic displacements with increasing strain, which is accompanied by an increase in the in-plane displacements. Reflecting the non-linear elastic properties of graphene, both trends together yield a non-monotonic variation of the total displacements with increasing tensile strain. This variation allows to test the role of nanometer-scale strain variations in limiting the carrier mobility of high-quality graphene samples.