Language Explorer supports lexical relations on lexical entries and senses.
In the screenshot, we are about to insert a synonym relation to the first sense of zazisa.
This brings up the following dialog, which lets us identify the entry and sense which is the synonym.
The lexical relation is added to both entries/senses, so if we now jump to the entry zaza we will find that the relation has been added there as well.
There are seven built-in relation types, and you can add your own.