To associate variations with the assembly, open the sequence (the sequence must be loaded) and drag it to the Assembly Reference Area:
<center> <br> <img src="/wiki/download/attachments/7667885/Associating Variations.png"/> <br> </center>
The variations will appear under the Consensus Sequence:
<center> <br> <img src="/wiki/download/attachments/7667885/Associating Variations_1.png"/> <br> </center>
To remove the association, select the Remove track from the view item in the Variations Area context menu.