Disappear, having crossed river in Japan? (7)
I believe the answer is:
varnish
'japan?' is the definition.
(I've seen this before)
'disappear having crossed river' is the wordplay.
'disappear' becomes 'vanish' (synonyms).
'having crossed' means one lot of letters goes inside another.
'river' becomes 'r'.
'vanish' enclosing 'r' is 'VARNISH'.
'in' acts as a link.
(Other definitions for varnish that I've seen before include "Hard finishing coating" , "Gloss finish" , "Wood or nail coating" , "'Hard, transparent coating (7)'" , "Japan" .)