In addition to using \uparrow as suggested in a comment, two instances of \stackunder had to be changed to \stackon.
Of course, this question/answer are based on Graphics equations: put text on equations
\documentclass{article}
\usepackage{graphicx}
\usepackage[usestackEOL]{stackengine}
\usepackage{xcolor}
\def\calloutsym{%
\ensurestackMath{%
\scalebox{1.7}{\color{red}\stackon[0pt]{\bigcirc}{\uparrow}}}%
}
\newcommand\callouttext[1]{%
\def\stacktype{S}\renewcommand\useanchorwidth{T}\stackText%
\stackon{\calloutsym}{\scriptsize\Longstack{#1}}\stackMath%
}
\newcommand\callout[3][1.5pt]{%
\def\stacktype{L}\stackMath\stackunder[#1]{#2}{\callouttext{#3}}%
}
\begin{document}
\[ K \callout{\subseteq}{by compactness} \bigcup_{J=1}^{n} V_{nJ} \]
\[ \lim_{n\rightarrow \infty} \int\limits_{x} f_{n} \mathrm{d}\mu
\callout[1.8pt]{=}{By Monotone\\Convergence Theorem} \int\limits_{x} f \mathrm{d}\mu
\]
\end{document}

ADDENDUM:
To handle both up and down callouts, just create tailored versions for each, invoked here with \upcallout[callout-vshift]{math item to callout}{callout text} and the corresponding \downcallout. REVISED to condense the code.
\documentclass{article}
\usepackage{graphicx}
\usepackage[usestackEOL]{stackengine}
\usepackage{xcolor}
\def\calloutsym{%
\ensurestackMath{%
\scalebox{1.7}{\color{red}\calloutstack[0pt]{\bigcirc}{\calloutarrow}}}%
}
\newcommand\callouttext[1]{%
\def\stacktype{S}\renewcommand\useanchorwidth{T}\stackText%
\calloutstack{\calloutsym}{\scriptsize\Longstack{#1}}\stackMath%
}
\newcommand\upcallout[3][1.5pt]{%
\def\calloutarrow{\uparrow}%
\def\calloutstack{\stackon}%
\def\stacktype{L}\ensurestackMath{\stackunder[#1]{#2}{\callouttext{#3}}}%
}
\newcommand\downcallout[3][1.5pt]{%
\def\calloutarrow{\downarrow}%
\def\calloutstack{\stackunder}%
\def\stacktype{L}\ensurestackMath{\stackunder[#1]{#2}{\callouttext{#3}}}%
}
\begin{document}
\[ K \upcallout{\subseteq}{by compactness} \bigcup_{J=1}^{n} V_{nJ} \]
\[ \lim_{n\rightarrow \infty} \int\limits_{x} f_{n} \mathrm{d}\mu
\downcallout[1.8pt]{=}{By Monotone\\Convergence Theorem} \int\limits_{x} f \mathrm{d}\mu
\]
\end{document}

\downarrowto an\uparrowon line 7. – Jul 07 '15 at 05:08