Assorted parameterization models for analysis of X-linked gene variants using the HAPLIN software.

X1 denotes the common allele and X2 the variant or target allele for a given SNP; ‘*’ denotes the product term; B represents the shared baseline risk for males and females; BM is the baseline risk for males only; BF is the baseline risk for females only; RR is the shared relative risk for males and females; RRM is the relative risk for males only; and RRF is the relative risk for females only. In Model 4, the risk for an X1X2 female is the average of the two homozygotes; i.e. (BF+BF*RR)/2 = BF(1+RR)/2. As this is not a log-linear model, HAPLIN replaces the heterozygous risk with BF√RR, i.e. the geometric mean of the two homozygous risks. Models 3 and 5 can be estimated assuming equal or unequal haplotype frequencies between males and females.