Table 1.

The configuration of two SNP combinations

Observed Genotype	Diplotype			Composite Diplotype
	Configuration	Frequency	Relative Freq.
11/11	[11][11]	$p_{11}^2$	1	HH
11/12	[11][12]	2 p11p12	1	$H\overline{H}$
11/22	[12][12]	$p_{12}^2$	1	$\overline{H}\overline{H}$
12/11	[11][21]	2 p11p21	1	$\overline{H}\overline{H}$
12/12	$\{\begin{array}{l}[11][22]\\ [12][21]\end{array}$	$\{\begin{array}{l}{p}_{11}{p}_{22}\\ p_{12}{p}_{21}\end{array}$	$\{\begin{array}{l}\varphi \\ 1-\varphi \end{array}$	$\{\begin{array}{l}H\overline{H}\\ \overline{H}\overline{H}\end{array}$
12/22	[12][22]	2 p12p22	1	$\overline{H}\overline{H}$
22/11	[21][21]	$p_{21}^2$	1	$\overline{H}\overline{H}$
22/12	[21][22]	2 p21p22	1	$\overline{H}\overline{H}$
22/22	[22][22]	$p_{22}^2$	1	$\overline{H}\overline{H}$

Where $\varphi =\frac{p_{11}{p}_{22}}{p_{11}{p}_{22}+p_{12}{p}_{21}}$