All Super Mario Run data (including any content you've purchased and any Rally Tickets you have) up to the moment you deactivate your account will be deleted from your device.
If you want to use Super Mario Run again, you will have to delete the game and reinstall it. You can then start using Super Mario Run from the beginning.
Note: After you deactivate a Nintendo Account, if you reactivate and relink your Nintendo Account within 30 days, your Super Mario Run data will be restored.