  Bi$_2$Se$_3$, a layered three dimensional (3D) material, exhibits topological
insulating properties due to presence of surface states and a band gap of 0.3
eV in the bulk. We study the effect hydrostatic pressure $P$ and doping with
rare earth elements on the topological aspect of this material in bulk from a
first principles perspective. Our study shows that under a moderate pressure of
P$>$7.9 GPa, the bulk electronic properties show a transition from an
insulating to a Weyl semi-metal state due to band inversion. This electronic
topological transition may be correlated to a structural change from a layered
van der Waals material to a 3D system observed at $P$=7.9 GPa. At large $P$
density of states have significant value at the Fermi-energy. Intercalating Gd
with a small doping fraction between Bi$_2$Se$_3$ layers drives the system to a
metallic anti-ferromagnetic state, with Weyl nodes below the Fermi-energy. At
the Weyl nodes time reversal symmetry is broken due to finite local field
induced by large magnetic moments on Gd atoms. However, substituting Bi with Gd
induces anti-ferromagnetic order with an increased direct band gap. Our study
provides novel approaches to tune topological transitions, particularly in
capturing the elusive Weyl semimetal states, in 3D topological materials.
