Through a two-stage association study using a total of 12 000 Japanese subjects, a novel locus, rs12946942 on chromosome 17q24.3, showed significant association and was replicated in a Han Chinese population.80 rs12946942 and the LD block containing it are in a gene desert between SOX9 and KCNJ2. The block contains six enhancer elements, one of which forms a long-range chromatin loop to SOX9 in a prostate cancer cell line, and SNPs within the enhancer appear to direct allele-specific gene expression. This evidence concerns the gene SOX9 and prostate carcinoma.