With stack
Version 1.4.0, Git revision e714f1d x86_64 hpack-0.17.0
on windows,
I ran
stack new simple
Thereafter, I changed the simple\stack.yaml file by inserting

ghc-variant: integersimple

after

resolver: lts-8.5

resulting in the following stack.yaml file (zipped)
stack.zip

After running stack setup,
I can run stack list-dependencies.
However, I get the wrong output:

Warning: File listed in simple.cabal file does not exist: README.md
base 4.9.1.0
ghc-prim 0.5.0.0
integer-gmp 1.0.0.1
rts 1.0
simple 0.1.0.0

I had not expect the dependency on integer-gmp, but a dependency on integer-simple!