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How do I set a user environment variable? (permanently, not session)

For a project I'm working on, I have a service that runs at startup which calls a script to set environment variables. This works just fine to set the variables before the login has occurred, however once the user logs in those environment variables are not being persisted and seem to dissappear. I currently have to call my script a second time from /etc/profile for the variables to be set after login. Is there a way to persist the environment variables across a login?

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