Several multiple, large-scale, genetic studies on autoimmune-disease-associated 
SNPs have been reported recently: peptidylarginine deiminase type 4 (PADI4) in 
rheumatoid arthritis (RA); solute carrier family 22 members 4 and 5 (SLC22A4 and 
5) in RA and Crohn's disease (CD); programmed cell death 1 (PDCD1) in systemic 
lupus erythematosus (SLE), type 1 diabetes mellitus (T1D), and RA; and protein 
tyrosine phosphatase nonreceptor type 22 (PTPN22) in T1D, RA, and SLE. Because 
these reports on association were not always evaluated in multiple ethnic groups 
and because ethnic difference in allele frequency of the variants has been also 
reported, we investigated allele frequencies of nine SNPs in four 
autoimmune-disease-associated loci in Caucasian, African-descent, and Japanese 
populations. Although SNPs in PADI4 had similar allele frequency among three 
groups [maximal difference 11%; (P >0.05)], the other three loci revealed 
statistically significant allele frequency differences (maximal difference 39% 
(P <0.00001), 13% (P <0.00001), and 8% (P <0.00001) in SLC22A4, PDCD1, and 
PTPN22, respectively). Of note, three SNPs in the three loci that had allele 
frequency more than 8% in the Caucasian population were either not polymorphic 
at all or extremely rare in the Japanese population. Our data suggest that 
ethnic variations of polymorphisms should be evaluated in detail, and 
differences should be incorporated into investigations of susceptibility 
variants for common diseases.