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Understanding the complex phase diagram of cuprate superconductors is a long-standing challenging problem. Recent studies have shown that orbital degrees of freedom, both Cu $e_g$ orbitals and O $p$ orbitals, are a key ingredient for a unified understanding of cuprate superconductors, including the material dependence. Here we investigate a four-band $d$-$p$ model derived from the first-principles calculations with the variational Monte Carlo method, which allows us to elucidate competing orders on an equal footing. The obtained results can consistently explain the doping dependence of superconductivity, antiferromagnetic and stripe phases, phase separation in the underdoped region, and also novel magnetism in the heavily-overdoped region. Our four-band $d$-$p$ model with neighbouring intersite interactions is a minimal model to describe the phase diagram comprehensively. The presence of $p$ orbitals is critical to the charge-stripe features, which induce two types of stripe phases with $s'$-wave and $d$-wave bond stripe. On the other hand, the presence of $d_{z^2}$ orbital is indispensable to material dependence of the superconducting transition temperature ($T_{\mathrm{c}}$), and enhances local magnetic moment as a source of novel magnetism in the heavily-overdoped region as well. These findings beyond one-band description could provide a major step toward a full explanation of unconventional normal state and high $T_{\mathrm{c}}$ in cuprate supercondutors.