\documentclass{article}
\usepackage{amsthm,amssymb,amsmath} 
\usepackage{xepersian} 
\settextfont[Scale=1.1]{XB Niloofar}
\begin{document}
\begin{equation}\label{eq:my} 
\[\begin{array}{*{20}{c}}
{\mathop W\nolimits_1 \in \mathop C\nolimits^{in} (X) \cup \mathop C\nolimits^{in} (Y)}\\
{\mathop W\nolimits_1  \notin \mathop C\nolimits_{in} (X) \cup \mathop C\nolimits_{in} (Y)}\\
{\mathop W\nolimits_1 \subseteq \mathop W\nolimits_0 }
\end{array}\]
باتوجه
\eqref{eq:my}
\end{equation}
\end{document}