Figure 3.

Extended Manhattan plot of μGWAS results for PTPRT (top), PPFIBP1 (bottom/left), and PTPRB (bottom/right) by AGP stage. The X-axis shows base pairs within chromosome. Black dots indicate significance in ssGWAS, lines indicate significance in diplotypes of width 2 (dotted) .. 6 (solid), red color indicates low μ-scores for reliability, suggesting a potential artifact, unless supported in both populations. Green dots and s-values indicate univariate results for SNPs within the most significant region. s-Values in gray indicate nearby results. Below the panels are gene annotations, LD blocks, and recombination rate from HapMap.⁸¹ The PTPRT region comprises rs6102794, rs6072693, rs6072694, rs6102795, rs6016759 and rs6102798. The ‘x' and box at the bottom indicate a somatic mutation at rs146825584⁷⁴ and a deletion at 41,036,259–41,300,521⁷³ (Supplementary Table S2, AU018704), respectively. The PTPRB: region comprises rs3782377, rs2567137, rs2567133, rs2278342, rs2116209 and rs2278341. KCNMB4 results driven by a single SNP in one population only (rs787931, red ‘x') are indicated as a potential artifact, but the related KCNMA1 was the most significant gene in AGP II (Table 1).