GWAS and a replication study examining CPD in 17,158 Japanese subjects. We assessed genome-wide single-nucleotide polymorphisms (SNPs) along with common copy number polymorphisms (CNPs) and identified haplotypes with a SNP and a CNP at the CYP2A6 locus that is a strong susceptibility variant for CPD and smoking-related diseases. Our study also estimated the heritability explained by the haplotype for CPD and smoking-related disease traits.