After controlling for rs2476601 using conditional haplotype analysis we found that it accounted for most of the association in PTPN22. However, even after conditioning on rs2476601 there was a modest association of rs1217414 with SLE. rs1217414 has been implicated in early onset psoriasis [57] and RA [58], [59] and may be involved in autoimmunity predisposition. Additionally, bioinfomatic search found that this SNP is potentially in an active promoter site for a chromatin regulatory site for B-lymphocyte cells [54].
