To identify rheumatoid arthritis (RA) susceptibility genes in a Japanese population by conducting a large‐scale case–control association analysis and linkage disequilibrium (LD) mapping on chromosome 7q31–34, a candidate susceptibility locus identified in a preliminary genome‐wide scan in 53 Japanese families, using single‐nucleotide polymorphisms (SNPs).

We prepared 728 dense, evenly spaced SNPs with a minor allele frequency >0.15 in each gene locus on chromosome 7q31–34. Using these SNPs, a 2‐stage case–control analysis was performed on 760 RA patients (157 men and 603 women) and 806 non‐RA controls (189 men and 617 women). Haplotypes and LD mapping results were assessed based on SNP genotypes in 380 controls.

Forty‐eight SNPs showed allele associations (P < 0.05) in the first set of DNA samples (380 RA cases and 380 non‐RA controls; first‐stage analysis). For 4 of the SNPs in the SEC8L1 gene, the association was replicated (P < 0.05) in the second, independent set of DNA samples (an additional 380 RA cases and 380 non‐RA controls; second‐stage analysis). When data from the 2 groups were combined, the most significant allele association was observed with SNP 441, an intronic SNP of the SEC8L1 gene (P = 0.000059). The SEC8L1 SNPs with significant allele associations were all located in a single conserved LD block (block 4). Haplotype analysis revealed the disease‐risk (P = 0.0015) and disease‐protective (P = 0.0000062) haplotypes. Resequencing of coding exons within block 4 did not identify any nonsynonymous SNPs. Real‐time quantitative polymerase chain reaction revealed that SEC8L1 was expressed ubiquitously in human tissues, including fibroblast‐like synoviocytes from RA patients.

Our locus‐wide association and LD analyses identified intronic SNPs and haplotypes in the SEC8L1 gene that are strongly associated with RA. We propose that SEC8L1, which encodes a component of the exocyst complex, is a candidate susceptibility gene for RA in the Japanese population.