You need to use the `&$expand=[Column internalname]` and the `&$Select=[Column internalname]/Id` url parameter to get the Id of the lookup item, if you need the text value from the lookup use /Title instead of /Id.

I have a lookup to a list, the column name in list which contains the lookup is "Sync", so my REST call is like this:

    /_api/web/lists(guid'1B51700E-D95D-46C5-9B9B-1386CCCC07DB')/items?$select=Title,Sync/Id&$expand=Sync

This returns the value from the column "Titel"and the id of the lookup column "Sync".