A Manhattan plot is a type of 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 In genomics, a genome-wide association study (GWA study, or GWAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on assoc ...

(GWAS) to display significant

SNPs In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...

. It gains its name from the similarity of such a plot to the

Manhattan Manhattan ( ) is the most densely populated and geographically smallest of the Boroughs of New York City, five boroughs of New York City. Coextensive with New York County, Manhattan is the County statistics of the United States#Smallest, larg ...

skyline A skyline is the wikt:outline, outline or shape viewed near the horizon. It can be created by a city's overall structure, or by human intervention in a rural area, rural setting, or in nature that is formed where the sky meets buildings or the ...

: a profile of

skyscrapers A skyscraper is a tall continuously habitable building having multiple floors. Most modern sources define skyscrapers as being at least or in height, though there is no universally accepted definition, other than being very tall high-rise bui ...

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 In mathematics, the logarithm of a number is the exponent by which another fixed value, the base, must be raised to produce that number. For example, the logarithm of to base is , because is to the rd power: . More generally, if , the ...

of the association ''p''-value for each

single nucleotide polymorphism In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...

(SNP) displayed on the ''y''-axis, meaning that each dot on the Manhattan plot signifies an 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 show the extent of each chromosome.

References

Statistical charts and diagrams Genetic epidemiology Single-nucleotide polymorphisms {{statistics-stub