It is a common practice that user attributes like phone number, departments etc are synchronized from Active Directory into User Properties within Jira.
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Luckily you can access the user properties in your email templates. References to user properties by property name must be prefixed with "jira.meta." as the Jira API requires a fully qualified name of the property.
E.g. If the user has a property, called "phone", the phone property of the current user may be rendered as
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$!userPropertyManager.getPropertySet($!currentUser).getString("jira.meta.phone") |
Instead of $!currentUser you can use any user objects from the issue, like: $!issue.assignee or $!issue.reporter.