Significant allelic association between PTPN22 was observed in EA and HS ( Table 1 ). In EA, 46 SNPs were associated (p<0.05) with SLE. The most significant association was with rs2476601 (P = 4.13×10−9, OR = 1.40 95% CI = 1.25–1.56) in EA. Intronic SNP rs1217414 was also significant in EA (P = 7.39×10−4, OR = 0.88 95% CI 0.82–0.95). Figure 1 shows the overall haplotype structure from select SNPs in this genomic region in EA including the two isoforms of PTPN22. All imputed SNPs from the PTPN22 region are shown in Figure S1. SNP rs2476601 was not significantly associated with SLE in HS (P = 0.20) and was monomorphic in AA and AS.
