We perform a global model-to-data comparison on Au+Au collisions at $\sqrt{s_{NN}}=200$ GeV and Pb+Pb collisions at $2.76$ TeV and $5.02$ TeV, using a 2+1D hydrodynamics model with the EKRT initial state and a shear viscosity over entropy density ratio $(\eta/s)(T)$ with a linear $T$ dependence. To quantify the amount of uncertainty due to the choice of the equation of state (EoS), we compare analysis results based on four different EoSs: the well known $s95p$ parametrisation, an updated parametrisation based on the same list of particles in hadron resonance gas, but using recent lattice results for the partonic part of the EoS, and two new parametrisations based on the Particle Data Group 2016 particle list and the recent lattice results. We find that the choice of the EoS does affect the favoured minimum value of $\eta/s$, although within the confidence limits of the analysis. On the other hand, our analysis hardly constrains the temperature dependence of $\eta/s$, no matter the EoS.