Figure 3

Linkage disequilibrium (LD) plots surrounding five genes involved in the vitamin D pathway in the SLSJ study. The LD plots were generated by Haploview 3.32 [41]. Gene symbols are indicated at the top of each graph. The top horizontal bar illustrates the location of SNPs on a physical scale. The color of squares illustrates the strength of pairwise r² values on a black and white scale where black indicates perfect LD (r² = 1.00) and white indicates perfect equilibrium (r² = 0). The r² LD value is also indicated within each square. Blocks are defined using the Gabriel et al [71] definition. Failed and monomorphic SNPs as well as SNPs not in Hardy-Weinberg equilibrium are not illustrated.