For the last several years, linkage disequilibrium (LD) mapping using single nucleo-tide polymorphisms (SNP) has revealed disease-susceptible variants for many common disorders, including myocardial infarction [1, 2] diabetes mellitus  and osteoarthritis . These findings have also been made for autoimmune diseases such as rheumatoid arthritis (RA) . It is of particular interest that independent study groups have reported that several genes are associated with multiple autoimmune disorders . Figure 1 summarises recent findings of disease-associated gene identification studies on autoimmune disorders and describes interrelations among multiple autoimmunities via disease-associated genes. In the following sections, the basics of SNP-based LD mapping and two major findings from the large-scale screening of RA-associated genes in a Japanese population are reviewed.
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