The lead SNP on chr1, rs6679677, is in high LD (r2 = 0.96) with a non-synonymous variant in exon 12 of the PTPN22 gene, a well-described genetic risk variant for autoimmune diseases (rs2476601, p = 2.82 × 10−24) (these are also the only two variants in the credible set; Supplementary Fig. 2). This evidence concerns the gene PTPN22 and autoimmune disease.