Figure 4

Representative kernel matrix plot of the IL10 gene in AA subjects. For each matrix, the ALI or non-ALI population of haplotypes is plotted against itself according to the kernel function. Each cell on the matrix reflects the extent of haplotype sharing between ALI subjects or non-ALI subjects. The cell size reflects the frequency of the haplotype, such that common haploypes are larger rectangles. The color reflects the kernel function value for each haplotype among ALI or non-ALI; more intense red coloration reflects a higher degree of similarity between pairs of subjects based on their diploid genotypes. Comparing the top and bottom plots in each box, one observes that the ALI (top) plots are distinct for each kernel function, but the plots are most discordant for the quadratic function, which allows for 2-way interactions between SNPs within the haplotype block to inform the association. Accordingly, the p- value for the quadratic kernel test with ALI was the most statistically significant.