We have developed efficient self-consistent 3D Schrödinger-Poisson solver to model the energy level spectrum in silicon quantum dots. We find that the energy level spectrum in the dot can be easily tuned by varying the applied voltage on the top and side gates, thus leading to symmetric or asymmetric parabolic confinement in the plane parallel to the semiconductor/oxide interface. We also investigate the influence of different impurity distributions in the semiconductor substrate on the shape of the wavefunctions and the energy spectrum in the dot. We noticed that different number and different distribution of the impurity atoms in the dot influences the energy spectrum by lifting degeneracy of the levels. We also observe significant mode mixing in the wavefunctions when using atomistic description of the impurity atoms in the semi conductor.