Linkage disequilibrium (LD) blocks within the BAFF gene. A schematic of the BAFF gene, TNFSF13B, is depicted at the top. The span of the 20 SNPs genotyped by Clark et al is demarcated by the genomic coordinates 109827503 and 108957942,¹  shown at the ends of the horizontal bracket immediately below the gene. Coordinates were taken from the most recent human gene build (hg19) visualized by the NCBI genome browser (http://www.ncbi.nlm.nih.gov). The 3 LD blocks depicted were determined using the confidence interval method with Hapmap 3 data implemented by Haploview 4.2.²  The rs numbers of the 4 Clark et al cGVHD SNPs, shown in the gray box, are within the same LD block (Block 2). Solid vertical lines indicate a SNP that was plotted by Haploview; and dashed lines, a SNP that was not. The LD plot generated by Haploview was modified so that it aligns with the gene schematic above it. Degree of LD between 2 SNPs can be visualized on the LD plot shown in this figure as follows: (1) locate the SNP at the top of the LD plot and then follow diagonally along the diamond shaped boxes to the intersection with the diagonal from the other SNP of interest. The SNPs in high LD are represented by the darkest diamond shaped boxes (pairwise D' values shown; black indicates D' ≥ 0.95); D' is a measure of the frequency of association of alleles at 2 loci. D' ranges from 0 to 1, with 0 representing random association and 1 representing absolute association.