Figure 4

The Haplotypes and Single Markers Associations displays. The Association tab contains three displays: Single Marker, Haplotypes, Permutation Tests. Top – The Haplotypes Association tab. For each block and each haplotype in a block a chi-square score is calculated (TDT test for pedigrees, case/control test for unrelated individuals) and a p-value is derived. Only haplotypes above a certain frequency threshold are considered and displayed (the threshold is set by the user in the Haplotypes tab). Bottom – The Single Marker tab for the same set of markers. In this example more significant associations are detected when testing for haplotype associations than when testing individual SNPs.