This is easily achievable by creating a line item which applies to Variance Version only.
There is one more method which might be of great help to you- functionality called Compare least used functionality in Anaplan which will let you compare the values or differences from Previous Version or List Items or Time.
In your case You can choose to compare your version with Previous Version or any Version of your choice.(Catch is that Anaplan will compare Current Version with Previous Version and also Previous Version with Previous - 1 Version) . For Example I have got three versions Actual, Forecast & Variance in the same order.
Step 1: Go to Module and Click on weighing scale option
Step 2: Select the Option
Output: It Compares Variance with Forecast and Forecast with Actual because that was the order of the versions.
Note: Compare is WS admin feature. Read more on Anapedia