So far we have scaled additive by additive epistatic interactions. A complete description, however, has to account for the effects of dominance as well. Dominance effects include within-locus dominance effects and, in the case of epistasis, the potential epistatic influence of the second locus of the within-locus dominance effects of the first locus and vice versa. Again, a distinction between the physiological and the statistical interpretation of dominance has to be made. Physiological dominance is defined as the deviation of the heterozygote phenotype value from the midway value of the two homozygote phenotype values at one locus (Cheverud and Routman, 1995). Statistical dominance deviations are deviations of single locus genotype values from a linear regression of the composing alleles to the genotypic values. As such, statistical dominance effects are dependent on the genotype frequencies in the population.
The within-locus dominance value 
at the A-locus can be defined as
the deviation of the heterozygote genotype value from the additive combination
of the physiological effects of the alleles and all additive-by-additive
epistatic components. It describes the within-locus dominance effects at the
A locus in the genetic background kl at the second locus and is given as:
where 
is the genotypic value predicted from the additive and AxA epistatic effects.
A similar equation holds for the within-locus genotype values at the B locus.
Next, the epistatic influence of the second locus on the dominance deviations
of the first locus is defined as:
Similar equations hold for the other locus. The dominance deviation of a
heterozygote genotype at A locus with an 
homozygote genotype at the
second locus is then given as:
This form of epistasis describes the additive components of the epistatic influence of the second locus on the dominance effects of the first locus. It captures the additive by dominance form of epistasis. In the case of the double heterozygote genotype additional effects can exist. There can be a ``dominance deviation of dominance effects'' or a second order dominance effect as well as an epistatic interaction between dominance effects. Unfortunately the two locus system is underdetermined for the double heterozygote genotype and we have to describe all those effects as the ``epistatically induced deviation of dominance effects'' in the double heterozygote genotype. It is defined as:
Taking the 
genotype as the starting point, all the genotype
values in the two locus two allele system can then be described in terms
of the values defined in Table 1.
Table 1: Complete description of the genotype values in a two locus two
allele system. The genotype values of a two locus two allele system are
expressed as a function of the reference genotype 
, the genotype
specific physiological effects of a gene substitution, 
, and
, the AxA epistasis coefficient
, the within-locus dominance values, 
, the values of the
epistatic influence of one locus on the dominance deviations of the other
locus, ed, and the ``epistatically'' induced deviation of dominance effects
in the double heterozygote genotype, 
.