Manhattan plot

A Manhattan plot is a type of scatter plot, usually used to display data with a large number of data-points, many of non-zero amplitude, and with a distribution of higher-magnitude values. The plot is commonly used in genome-wide association studies (GWAS) to display significant SNPs.[1]

An illustration of a Manhattan plot depicting several strongly associated risk loci

It gains its name from the similarity of such a plot to the Manhattan skyline: a profile of skyscrapers towering above the lower level "buildings" which vary around a lower height.

GWAS

In GWAS Manhattan plots, genomic coordinates are displayed along the X-axis, with the negative logarithm of the association P-value for each single nucleotide polymorphism (SNP) displayed on the Y-axis, meaning that each dot on the Manhattan plot signifies a SNP. Because the strongest associations have the smallest P-values (e.g., 10−15), their negative logarithms will be the greatest (e.g., 15). The different colors of each block usually shows the extent of each chromosome.

References
  1. Gibson, Greg (2010). "Hints of hidden heritability in GWAS". Nature Genetics. 42 (7): 558–560. doi:10.1038/ng0710-558. PMID 20581876.


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