Table 1.

Example Haplotype Frequencies for Disease and Marker Loci and Calculation of the Risk Ratio of the Marker

Frequency	D = 0	D = 1	Total	Pr(Y = 1,D,M)	D = 0	D = 1	Total	RR(M)
M = 0	0.9	0	0.9		0.9	0	0.9	1.0
M = 1	0.05	0.05	0.1		0.05	0.1	0.15	1.5

Abbreviations are as follows: D, allele at causal variant; M, allele at marker locus; Y, disease phenotype. Risk ratio (RR) of D = 1 is 2. Pr(Y = 1,D,M) is relative to a baseline that cancels in the marker risk ratio; see Appendix A for details of calculations.