For brevity, we will refer to the haplotype with A = i and B = j as ij. Consider the population distribution of the four possible haplotypes formed by the two SNPs; three parameters are necessary to represent an arbitrary distribution. Together with fA and fB, we use the population correlation coefficient to fully parameterize this distribution. The square of this is a commonly used measure of LD, usually denoted by r2 [e.g. Zondervan and Cardon, 2004].
