Shared loci: Association results for SLE susceptibility loci associated with another autoimmune disease.

Only the most significant variant in each region is presented. All variants met a FDR-adjusted threshold of significance in the joint-analysis (FDR P<0.05), as described in the Materials and Methods. The genomic control-adjusted (GC) P-value is also shown. When both joint and LLAS1 results available, a meta-analysis between all cohorts is presented. The smallest P-value is presented and, unless noted otherwise, it is under the additive model. OR and CI calculated under the model presented. Ch – chromosome; Mb – Megabases; MA – minor allele; MAF – Minor allele frequency; OR – odds ratio; CI – confidence interval; NA – not available. *This marker failed quality control or was unavailable in the joint-analysis, here we are presenting the LLAS results. 1The initials after the marker denote that this marker was imputed in a cohort: SSLEGEN, MMN, UUCSF. 2The superscript after the P-value denotes its genetic model, when other than the additive: ddominant, rrecessive. 3Diseases that reported any associated SNP in Caucasians with P-value<1.0×10−5 in the regions indicated (not necessarily the same SNP reported in this table) through the GWA approach [28]. Disease abbreviations are the same as for Table 1.