Figure 1: Regional association plot for genotyped and imputed SNPs at 17q21.31. | Nature Communications

Figure 1: Regional association plot for genotyped and imputed SNPs at 17q21.31.

From: Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

Figure 1

The middle portion of the plot contains the region of the inversion polymorphism (ch 17: 43,624,578–44,525,051, hg build 37), with the four blue dots representing the candidate miRSNPs (rs4640231, rs1052587 and rs17574361) and the tagSNP, rs916793. rs1052587 in the 3′UTR of MAPT has the strongest signal (P=4.6 × 10−8) among the miRSNPs. The cluster on the left side of the plot (around 43.5 MB) contains highly correlated SNPs (r2=0.99), including three directly genotyped intronic SNPs, rs2077606 and rs17631303 in PLEKHM1 (P=3.9 × 10−10 and P=4.7 × 10−10, respectively), and rs12942666 in ARHGAP27 (P=1.0 × 10−9). The LD between each plotted SNP and the top-ranked SNP in the region with the best clustering, rs12942666, is depicted by the colour scheme; the deeper the colour red, the stronger the correlation between the plotted SNP and rs12942666. The top miRSNP, rs1052587, is moderately correlated (r2=0.76) with rs2077606, rs17631303 and rs12942666 in our study population (n=8,371 invasive serous cases and n=23,491 controls, of European ancestry).

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