To test for a haplotype-specific effect, we compared a 3-d.f. haplotype-based test with the 2-d.f. locus-based test. The 3-d.f. haplotype-based test was performed by adding a numerical indicator variable for the ‘interaction’ term to the 2-d.f. locus-based model: coding the indicator variable as 0, 1 or 2, representing the number of occurrences of the G.G haplotype. However, this interaction term often depends on the (unobserved) haplotype phase, so for the case-control analysis, we replace this indicator variable by its expectation under the null hypothesis, θ / (1 + θ), where θ is the odds ratio measure of association between the rs1893217(G>A) and rs478582(G>A).
