Figure 2. Annotation strategy for the significant variants and their proxies.

The figure shows the detailed strategy of our annotation approach used to prioritize functional SNPs. HaploReg v4.1 (http://www.broadinstitute.org/mammals/haploreg/haploreg.php) was used to search proxies (r² ≥ 0.8 in Asian) of the associated SNPs and their binding motifs and epigenetic marks. The rSNPBase (http://rsnp.psych.ac.cn/) database was used to search for regulatory SNPs with experimentally validated regulatory elements controlling transcriptional and post-transcriptional events. RegulomeDB (http://www.regulomedb.org/) was used to search for the regulatory scores of SNPs according to their amount of regulatory information. Abbreviations: eQTL: expression quantitative trait locus; GWAS: genome-wide association study; rSNP: regulatory single nucleotide polymorphism; SLE: systemic lupus erythematosus; SNP: single nucleotide polymorphism.