The only kind of reference that is suported in yEd is through the URL property of nodes and edges. See the section on URL and Description in chapter Properties of Graph Elements in the yEd Manual for more information. If the URL property points to a GraphML file, you can use "View" -> "Go to URL" or F8 to quick open the referenced file in yEd.
I.e. suppose you have your core model saved as GraphML file, then you could create a node in your variation models that represents the core model and set the representative's URL property to point to the GraphML file with the core model.