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. We would not anticipate this degree of clustering if the results were solely due to chance. The Monte Carlo p values noted here are thus 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.
