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, for instance in genome-wide association studies

Genome-wide association study

In genetic epidemiology, a genome-wide association study , also known as whole genome association study , is an examination of many common genetic variants in different individuals to see if any variant is associated with a trait...

 (GWAS). In GWAS Manhattan plots, genomic coordinates are displayed along the X-axis, with the negative logarithm

Logarithm

The logarithm of a number is the exponent by which another fixed value, the base, has to be raised to produce that number. For example, the logarithm of 1000 to base 10 is 3, because 1000 is 10 to the power 3: More generally, if x = by, then y is the logarithm of x to base b, and is written...

 of the association P-value for each single nucleotide polymorphism

Single nucleotide polymorphism

A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...

 displayed on the Y-axis. Because the strongest associations have the smallest P-values (e.g., 10^-15), their negative logarithms will be the greatest (e.g., 15).

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

Manhattan

Manhattan is the oldest and the most densely populated of the five boroughs of New York City. Located primarily on the island of Manhattan at the mouth of the Hudson River, the boundaries of the borough are identical to those of New York County, an original county of the state of New York...

 skyline

Skyline

A skyline is the overall or partial view of a city's tall buildings and structures consisting of many skyscrapers in front of the sky in the background. It can also be described as the artificial horizon that a city's overall structure creates. Skylines serve as a kind of fingerprint of a city, as...

: a profile of skyscrapers towering above the lower level "buildings" which vary around a lower height.