7.7 Manhattan plots

Manhattan plots show the distribution of GWAS hits across the genome, where the y-axis is p-value.
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Fig. 6. Manhattan plot of GWAS results. The red line is the \(5*10^{-8}\) genome-wide significance threshold.

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Why are there peaks in the Manhattan plot?

Each peak is composed of variants from the same haplotype, which all have a strong association with the phenotype because of LD.

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