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Background  Non-coding single nucleotide polymorphisms within the nicotinic acetylcholine receptor alpha 4 subunit gene  (CHRNA4)  are robustly associated with various neurological and behavioral phenotypes including schizophrenia, cognition and smoking. The most commonly associated polymorphisms are located in exon 5 and segregate as part of a haplotype. So far it is unknown if this haplotype is indeed functional, or if the observed associations are an indirect effect caused by linkage disequilibrium with not yet identified adjacent functional variants. We therefore analyzed the functional relevance of the exon 5 haplotype alleles.    Results  Using voltage clamp experiments we were able to show that the  CHRNA4  haplotype alleles differ with respect to their functional effects on receptor sensitivity including reversal of receptor sensitivity between low and high acetylcholine concentrations. The results indicate that underlying mechanisms might include differences in codon usage bias and changes in mRNA stability.    Conclusions  Our data demonstrate that the complementary alleles of the  CHRNA4  exon 5 haplotype are functionally relevant, and might therefore be causative for the above mentioned associations.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0204-1) contains supplementary material, which is available to authorized users.

The nicotinic acetylcholine receptor alpha 4 subunit contains a functionally relevant SNP Haplotype