We would anticipate the observed, highly significant clustering of SNPs that display nominally positive results if many of these reproducibly positive SNPs lay near and were in linkage disequilibrium with functional allelic variants that distinguished substance dependent subjects from control subjects, but not if they represented chance observations. The Monte Carlo p values noted here are likely to receive contributions from both the extent of linkage disequilibrium among the clustered, nominally positive SNPs and the extent of linkage disequilibrium between these SNPs and the functional haplotype(s) that lead to the association with substance dependence.
