Based on the local sequence around these SNPs, there are several putative functional elements that may be affected by different alleles. The 5’ UTR of CHRNB3 shows evidence for a variety of putative transcription factor binding sites (as predicted by Transcriptional Element Search System: http://www.cbi.upenn.edu/tess). In particular rs4950 appears to be in close proximity to a binding site of the ubiquitous trans-activator AP1 (ID:T00029). In the case of CHRNA6 there are numerous predicted transcription factor binding sites, particularly near the SNPs in intron 2, but none of note near rs2304297. Polymorphisms such as rs2304297 would be more likely to effect expression through trafficking of mRNA, miRNA binding, and/or rate of degradation since it is the 3’ UTR (Brant-Zawadzki et al, 2007; Maziere and Enright, 2007).
