SNPs in the HAB/LAB AVP promoter confer differential allele-specific transcription in vivo. A, Scheme of the rat AVP promoter region. This region, containing 2799 bp, harbors 10 SNPs. The T(+549)C polymorphism, which was used to determine allelic-specific transcription in vivo, locates in intron 1. B, Scheme of the allele-specific transcription method. A heterozygote animal contains a promoter allele from both the HAB and LAB lines expressed in the same PVN neurons. A transcribed polymorphism localized to the same allele as a putative regulatory polymorphism in the promoter can be used to track the promoter allele from which the mRNA was transcribed. RNA extracted from the PVN is used in reverse transcription-PCR and subcloning, and sequencing of the resulting products yields a precise measure of the efficiency by which either allele was transcribed in vivo. C, Allelic transcription rate for AVP in the PVN evidenced a 60:40 ratio in favor of the HAB allele. In situ hybridization data from the HAB and LAB PVN also demonstrate higher levels of AVP mRNA in the HAB animal, which correlates well with the higher activity of the AVP promoter. ^**p < 0.005. D, Allelic transcription rate for oxytocin in the PVN demonstrated a 50:50 ratio for the oxytocin transcription rates, in agreement with the in situ hybridization data demonstrating no difference between the HAB and LAB lines.