The effect of the intronic risk SNP rs1344706 genotypes on ZNF804A allelic expression was analyzed. The allele-specific expression differences can be identified by comparing the relative levels of exonic SNP alleles (A and T) in RNA samples from subjects heterozygous for rs12476147. We measured the allelic specific expression (ASE) of the rs12476147 coding variant, located in the last exon of the full-length ZNF804A mRNA (NM_194250), and in strong LD with rs1344706. To make sure the ASE assay was accurate, we first quantified the two alleles at SNP rs12476147 in genomic DNA mixes with known ratios. The observed ratio presented a highly linear relation with the expected ratio (r2 = 0.99), thus confirming that our assay could be used to differentiate two alleles, in the range of 0.125 – 8 A/T ratio (data not shown).
