Figure 2. Manhattan plot of associations between SNPs and ER status restricted to HER2− cases.
P-values from logistic regression comparing estrogen receptor positive cases to estrogen receptor negative cases restricted to HER2− cases, controlling for age at diagnosis and first two principal components, are shown. rs2981578 on chromosome 10 at the FGFR2 locus shows the strongest association. The same 914144 SNPs were included in these analyses, with 4267 HER2-/ER+ and 1185 HER2-/ER- cases. The red horizontal line corresponds to the empirical significance threshold of 1.48×10−7, while the blue horizontal line corresponds to an arbitrary level of 1.0×10−5. The inflation factor (λ) for these analyses is 1.02.