We identified 31 unique single-nucleotide variants in the coding exons and flanking intronic regions of CHRNA4 in the discovery cohort. Of these variants, 21 were exonic, including 8 types of SNPs (minor allele frequencies (MAF) > 5%) and 13 types of rare variants (MAF ≤ 1%, Figure 1A). None of the variants were found to have MAF between 1% and 5%. Six of the 13 rare variants identified were nonsynonymous substitutions, and all were missense mutations. Two individuals from the control group seemed to be homozygous for rare nonsynonymous variants. However, due to the rarity of these variants, the probability of being homozygous is low; it is possible that these two controls had a deletion (e.g., an overlapping CNV) in one chromosome over that region. The following statistical analyses considered these “homozygous” sites as monoallelic, to be conservative. In total, we observed 11 rare nonsynonymous variants (Table 1), which did not differ in frequency between cases and controls (FET p=0.56, WSM p=0.30).
