Too many possibilties are coming to mind.
The phenotype brought about by a certain genotype can be affected by another genotype on different chromosomes. For example, in a mouse, there are alleles (which are genes) that can cause the brown color or the black color. Black is dominant over brown, but there are other alleles on different chromosomes that can affect how this genotype will be expressed.
There are alleles that determine if the genes that code for the brown or black color will even be active. The allele that causes them to be active is dominant, and the allele that causes them to be useless are recessive. If both recessive alleles are inherited, then neither brown nor black will be seen. Just white!
This is an example of epistasis.