Fig. 2: Manhattan plot of the multi-ancestry and multi-trait SLE GWAS meta-analysis.

We consider loci reported in the GWAS catalog (as of 12/11/2021) or in the studies used in our meta-analysis as known (brown). We define novel loci (green) as the ones that are 1 million base pairs away from previously reported GWAS loci. Diamonds in the plot represent sentinel variants at novel loci. Diamond with black outline represents novel loci that are replicable according to RATES. In total, we identify 79 known loci and 27 novel loci, of which 74 known loci and 16 novel loci are deemed replicable (PPR > 0.90) by RATES. We also annotated the target genes for top variants at each novel locus using Open Targets Genetics database. Here, y axis is truncated at P value = 1 × 10⁻¹⁸ to visualize the novel loci. The red line represents the genome-wide significance level (5 × 10⁻⁸). Two-sided P value associated with each variant is calculated according to the Chi-squared test statistic with 1 degree of freedom.