(A) Manhattan plot of the association of iChip variants with autoantibody-positive RA in African Americans. The x-axis indicates chromosome and position, the y-axis indicates association strength −log(p). The blue line illustrates suggestive statistical association (p = 1*10−4). The red line illustrates iChip-wide level of statistical significance (p = 3.1*10−6). (B) Conditional analysis in the extended MHC region (chr6:26,000,000–34,000,000). Axes have the same meanings as in (A). Red, green and blue dots are SNPs in the regions immediately surrounding HLA-DRB1, HLA-DPB1 and HLA-B, respectively. The left panel shows the association summary statistics before conditioning on HLA-DRB1 alleles. The strongest association maps to HLA-DRB1. The right panel shows the locus after conditioning on HLA-DRB1 4-digit alleles.