Open Access Research article

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

Fiona Gee*, Clare F Clubbs, Emma VA Raine, Louise N Reynard and John Loughlin

Author Affiliations

Institute of Cellular Medicine, Musculoskeletal Research Group, Newcastle University, Newcastle-upon-Tyne, UK

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BMC Medical Genetics 2014, 15:53  doi:10.1186/1471-2350-15-53

Published: 4 May 2014

Additional files

Additional file 1:

Table of patient characteristics and their genotype at rs6976.

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Additional file 2:

The seven transcript SNPs and their pair-wise D’ and r2 values relative to rs6976.

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Additional file 3:

Primer sequences used for genotyping and allelic expression analysis.

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Additional file 4:

Association analyses of transcript SNP proxies in NT5DC2 and POC1A with osteoarthritis using arcOGEN data.

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Additional file 5:

Allelic expression analysis in joint tissue from osteoarthritis (OA) patients. Allelic expression was assessed using the transcript single nucleotide polymorphisms (SNPs) (A) rs11177, (B) rs6617, (C) rs17264436, (D) rs6976, (E) rs7639267, (F) rs6769789 and (G) rs747343. Allelic expression of cDNA was normalised to its corresponding DNA. Data is presented as a ratio of expression of the major allele over that of the minor allele; hence a value above 1 means that there is less of the OA-associated allele. Samples are grouped according to the genotype at the OA-associated SNP rs6976, which are shown. Error bars represent the standard error of the mean. FP, fat pad; Sy, synovium; Me, meniscus; Li, ligament.

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