The allelic state of the genotype at a particular locus is coded either as 1,2, or 3 if the locus is homozygous for the susceptibility allele, heterozygous for both alleles, or homozygous for the non-susceptibility allele, respectively. According to the number of states the genotype can assume, an equal number of phenotypic values must be set. After assessing the state l of an individual's genotype at the causative loci, the actual value of the quantitative phenotypic expression of the present genotype is randomly drawn from a Gaussian distribution: where l designates the mean phenotypic effect of the l-th genotype and σ the homoscedastic phenotypic variance. The mean effects for every genotypic state, (μ_l,...,μ_3L), and σ must be specified. By setting σ = 0, the phenotypic values assume exactly the mean genotypic effects. They have to be specified in the following order:

• If there is only one susceptibility locus, the sequence is simply: a1 a2 a3 for two loci, the first (left) locus is fixed at first and the second (right) locus assumes all possible allelic states subsequently. Then the first locus assumes its second allelic state while the second locus assumes all its states et cetera:
  a11 a12 a13 a21 a22 a23 a31 a32 a33
• The general order to specify the penetrances is:
  a1...111 . . . a1...113 a1...121 . . . a1...133 a1...211 . . . a3...323 a3...331 a3...332 a3...333
• Example for input:
  12 25 14 -3 ... or 25;13;12,3;4.5; ...