To further examine the relationship between our top variant identified for DSM-5 cocaine use disorder and the group of variants known to be associated with smoking tagged by rs1451240, we performed haplotype-based association testing using rs9298626 and rs1451240. These two SNPs occur on three haplotypes that occur with a frequency >1% (Table 4). We chose rs1451240 because it was found to be genome-wide significant for nicotine dependence in a previous study using the SAGE GWAS data23. The most common haplotype, composed of the major alleles of both SNPs, has a frequency of 78%. The haplotype associated with the highest risk for DSM-5 cocaine use disorder, has a frequency of 4% and is composed of the minor alleles at both rs9298626 and rs1451240 (OR = 3.19 p = 1.35 × 10−4, 95% CI = 1.64–4.73). A haplotype composed of the major allele at rs9298626 and the minor allele at rs1451240 has a frequency of 18% but was not associated with DSM-5 cocaine use disorder (p = 0.14). Because the frequencies and odds ratio of the haplotype with both minor alleles is
