There are two common ways to visualize the extent of LD between pairs of loci. LD decay plots are used to visualize the rate at which LD declines with genetic or physical distance (Figure 2). Scatter plots of r2 values versus genetic/physical distances between all pairs of alleles within a gene, along a chromosome, or across the genome are constructed. Alternatively, disequilibrium matrices are effective for visualizing the linear arrangement of LD between polymorphic sites within a gene or loci along a chromosome (Figure 3). It should be noted that LD decay is unpredictable. Both plot types highlight the random variation in LD owing to a variety of forces discussed below.