Since the rs12476147 SNP is in strong, but not perfect, LD with the rs1344706 SNP, we were able to test the effect of the rs1344706 genotype on ZNF804A allelic expression of rs12476147. The 46 rs12476147 heterozygotes were further divided into 2 groups based on the rs1344706 homozygous AA (N=19) and heterozygous CA (N=27) genotypes. cDNA allele A/T ratios were significantly different depending on the intronic rs1344706 genotypes (AA vs CA, p-value = 0.03). In the rs1344706 heterozygous group the cDNA allele ratio was significantly higher than the genomic DNA allele ratio (average 1.06, 95% CI 1.02-1.09; p-value = 0.02), whereas in rs1344706 homozygotes, cDNA allele ratios did not differ from the genomic DNA allele ratios (average 1.00, 95% CI 0.96-1.03; p-value=0.87).
