Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies

Jiabo Wang, Jianming Yu, Alexander E. Lipka, Zhiwu Zhang

Research output: Chapter in Book/Report/Conference proceedingChapter


With increasing marker density, estimation of recombination rate between a marker and a causal mutation using linkage analysis becomes less important. Instead, linkage disequilibrium (LD) becomes the major indicator for gene mapping through genome-wide association studies (GWAS). In addition to the linkage between the marker and the causal mutation, many other factors may contribute to the LD, including population structure and cryptic relationships among individuals. As statistical methods and software evolve to improve statistical power and computing speed in GWAS, the corresponding outputs must also evolve to facilitate the interpretation of input data, the analytical process, and final association results. In this chapter, our descriptions focus on (1) considerations in creating a Manhattan plot displaying the strength of LD and locations of markers across a genome; (2) criteria for genome-wide significance threshold and the different appearance of Manhattan plots in single-locus and multiple-locus models; (3) exploration of population structure and kinship among individuals; (4) quantile–quantile (QQ) plot; (5) LD decay across the genome and LD between the associated markers and their neighbors; (6) exploration of individual and marker information on Manhattan and QQ plots via interactive visualization using HTML. The ultimate objective of this chapter is to help users to connect input data to GWAS outputs to balance power and false positives, and connect GWAS outputs to the selection of candidate genes using LD extent.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages18
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • False positive rate
  • GWAS
  • Kinship
  • Linkage disequilibrium
  • Mixed linear model
  • Population structure

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


Dive into the research topics of 'Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies'. Together they form a unique fingerprint.

Cite this