Haploview allows you to bounce back and forth between the LD plot and the block definitions and the haplotypes and frequencies for the currently defined blocks. Click on the Haplotypes tab or select the Haplotypes display from the Display menu to view haplotypes. Shown below are haplotypes using the default blocks in the sample dataset. Marker numbers are shown across the top, with tag SNPs highlighted with a triangular pointer. Note that these tag SNPs are not an optimized set for the entire region (more information available in the documentation). Population frequencies are shown next to each haplotype and lines show the most common crossings from one block to the next, with thicker lines showing more common crossings than thinner lines. Shown beneath the crossing lines is multilocus D prime, which is a measure of the LD between two blocks. The closer to zero the value is, the greater the amount of historical recombination between the two blocks.

The threshold of haplotypes to be shown, as well as the cutoffs for the connecting lines can be edited using the panel at the bottom of the screen. Alleles can also be displayed numerically or as colored boxes using the checkbox in the control panel.