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Background  An osteoarthritis (OA) susceptibility locus has been mapped to chromosome 3p21, to a region of high linkage disequilibrium encompassing twelve genes. Six of these genes are expressed in joint tissues and we therefore assessed whether any of the six were subject to  cis -acting regulatory polymorphisms active in these tissues and which could therefore account for the association signal.    Methods  We measured allelic expression using pyrosequencing assays that can distinguish mRNA output from each allele of a transcript single nucleotide polymorphism. We assessed RNA extracted from the cartilage and other joint tissues of OA patients who had undergone elective joint replacement surgery. A two-tailed Mann–Whitney exact test was used to test the significance of any allelic differences.    Results   GNL3  and  SPCS1  demonstrated significant allelic expression imbalance (AEI) in OA cartilage ( GNL3 , mean AEI = 1.04,  p  = 0.0002;  SPCS1 , mean AEI = 1.07,  p  < 0.0001). Similar results were observed in other tissues. Expression of the OA-associated allele was lower than that of the non-associated allele for both genes.    Conclusions   cis -acting regulatory polymorphisms acting on  GNL3  and  SPCS1  contribute to the OA association signal at chromosome 3p21, and these genes therefore merit further investigation.

Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1