Linkage disequilibrium (LD) block mapped by CTL-2A12 and CTL-1B9. (A) An LD block map identified by pairwise r2 plot from HapMap CEU data are overlayed with SNPs available from Affymetrix GeneChip SNP-genotyping microarrays (arrows) and 4 genes in the 115 kb block. SNPs that emerged repeatedly in the 2 independent experiments are indicated in blue. The genomewide P values for positive SNPs are shown as follows: *P < .05; **P < .01; ***P < .001. The intronic SNP (rs9945924) controlling the alternative splicing of HMSD transcripts and expression of encoded ACC-6 minor H antigen is indicated in red. (B) LD blocks identified by pairwise r2 plot from HapMap JPT data are overlayed with SNPs available from Affymetrix GeneChip SNP-genotyping microarrays (arrows) and exon 1 of the BCL2A1 gene. The only SNP showing a high association with CTL-1B9 immunophenotypes (rs1879894) is shown as an open arrow. The nonsynonymous SNP (rs1138357) controlling the expression of the minor H antigen recognized by CTL-1B9 is indicated by a red arrowhead. ***SNP with genomewide P < .001. The 2 SNPs adjacent to the 26 kb LD block (rs2562756 and rs6495463) never gave a significant genomewide P value.
