Our reciprocal polygenic analyses suggested that there were some shared genetic liability between schizophrenia and ND as defined by the FTND and COT traits. We then proceeded to identify the variants associated with both schizophrenia and ND traits. We computed joint P-values for each marker using the summary statistics from the schizophrenia and COT/FTND/TFC meta-analyses, and assigned a q-value to each of the joint P-values using an FDR method2425. Table 3 listed the loci identified by the joint analyses with q-values ≤ 0.05. From the joint analyses between schizophrenia and COT, 11 loci reached genome-wide significance for association with both COT and schizophrenia, of which 2 loci had no known genes nearby and 6 were spliced ESTs or long non-coding RNAs. In the analyses between schizophrenia and FTND, 10 loci were identified, and 3 of them were ESTs or non-coding RNAs. The joint analyses between schizophrenia and TFC yielded 15 significant loci. The CHRNA5-CHRNA3-CHRNB4 locus was the only one identified by all three smoking traits. In addition to some genes known to be associated with schizophrenia (HLA-B and MAD1L1), we
