qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

Summary Genome-wide association studies (GWAS) have identified thousands of human trait-associated single nucleotide polymorphisms. Here, I describe a freely available R package for visualizing GWAS results using Q-Q and manhattan plots. The qqman package enables the flexible creation of manhattan plots, both genome-wide and for single chromosomes, with optional highlighting of SNPs of interest. Availability qqman is released under the GNU General Public License, and is freely available on the Comprehensive R Archive Network (http://cran.r-project.org/package=qqman). The source code is available on GitHub (https://github.com/stephenturner/qqman). Contact turner@virginia.edu

• Publication year

  2014

• Venue

  bioRxiv

• Publication date

  2014-05-14

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1101/005165
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

  2013cited by this paper
• LocusZoom: regional visualization of genome-wide association scan results

  2010cited by this paper
• PLINK: a tool set for whole-genome association and population-based linkage analyses.

  2007cited by this paper
• Haploview: analysis and visualization of LD and haplotype maps

  2005influential reference

• Genomic insights into egg production in Mahuang chickens: identification of key loci and candidate genes through whole genome sequencing and validation.

  2026cites this paper
• A new genetic architecture for PHS resistance in rice: deciphering the epistatic interactions of three major QTL.

  2026cites this paper
• A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation

  2026cites this paper
• CMTM8 variants influence BNT162b2 COVID-19 vaccination response by regulating granulocytic/polymorphonuclear myeloid-derived suppressor cell activity

  2026cites this paper
• Gene variants in the pheromone vomeronasal receptors and QTLs around behavioral and fat metabolism genes associated with altered feed efficiency in cattle

  2026cites this paper
• R-loop editing by DNA cytosine deaminase APOBEC3B modulates the activity of oestrogen receptor enhancers.

  2026cites this paper
• Modulation of Avian Iridescence via Melanogenesis

  2026cites this paper
• Exploring the genetic architecture underlying dietary fiber content in Colombian Andean blueberry (Vaccinium meridionale Swartz)

  2026cites this paper
• Digitaria genome analyses indicate introgression may drive local adaptation and herbicide resistance.

  2026cites this paper
• Sequence-based genome-wide association study reveals genetic and metabolic mechanisms underlying feed efficiency-related traits in beef cattle

  2026cites this paper
• Genomic variants distinguish Pseudomonas aeruginosa from cystic fibrosis sputum and bloodstream infection

  2026cites this paper
• A Genome-Wide Association Study of Colorectal Cancer Mortality Outcomes Among Individuals of African and Admixture Ancestry.

  2026cites this paper
• Genome-wide association study uncovers the genetic basis of stem rust resistance in the southern US oat (Avena sativa L.) germplasm at different growth stages

  2026cites this paper
• Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics.

  2026cites this paper
• Content characteristics and genetic architecture of macronutrient signatures in cottonseed

  2026cites this paper
• Pharmacogenomic predictors of drug response and choice in dyslipidemia and hypertension

  2026cites this paper
• European taurine vs indian indicine cattle: a comparative genomic study reveals regions of differentiation during evolution and selection during crossbreeding

  2026cites this paper
• Ellagic Acid Seed Priming Reconfigures Polygenic Networks to Harmonize Antioxidant Defense and Growth in Barley Under UV-B Radiation: Insights from Genome-Wide Association Study

  2026cites this paper
• Integrating SEM-Based Phenotyping with GWAS Reveals the Genetic Architecture of Rice Straw Secondary Cell Wall and Internode Cell Features.

  2026cites this paper
• Ethnic‐specific effects of the LILRB2–LILRB5 locus and newly identified risk loci for Alzheimer's disease in the East Asian population

  2026influential citation
• Genome-Wide Meta-Analysis of 1 896 991 Individuals Identifies 31 Novel Risk Loci for Iron Deficiency Anemia.

  2026cites this paper
• Indian‐enriched genetic variants are associated with cognitive function

  2026cites this paper
• Genome-wide interaction analysis of long-term trihalomethane exposure in drinking water and colorectal cancer risk in a Spanish Multicenter Case-Control Study (MCC-Spain).

  2026cites this paper
• Analysis of Genetic Variation of Rice Straw Characteristics and Its Influence on Biomass

  2026cites this paper
• Identification of a genetic risk factor for metformin-induced vitamin B12 deficiency

  2026influential citation
• A drought stress-induced MYB transcription factor regulates pavement cell shape in leaves of European aspen (Populus tremula)

  2026cites this paper
• GENOVIS: a Python package for the visualization of population genetic analyses

  2026influential citation
• Exploring the genetic diversity of Mediterranean fig trees highlights genes associated with fruit traits.

  2026cites this paper
• Genomic prediction of superior heartwood traits in pedunculate oak (Quercus robur L.) using GWAS-informed Bayesian models

  2026cites this paper
• selscape: A Snakemake Workflow for Investigating Genomic Landscapes of Natural Selection

  2026cites this paper
• Population Structure of Genotypes and Genome-Wide Association Studies of Cannabinoids and Terpenes Synthesis in Hemp (Cannabis sativa L.)

  2026cites this paper
• Characterization of the genetic architecture of adult plant resistance to sharp eyespot in Chinese wheat germplasm

  2026cites this paper
• Genome-wide association and functional genomic analyses of teat placement traits derived from robotic milking systems in American Holstein cattle.

  2026cites this paper
• Deciphering the ceRNA Network in Alfalfa: Insights into Cold Stress Tolerance Mechanisms.

  2026cites this paper
• Genome-wide association study of major anxiety disorders in 122,341 European-ancestry cases identifies 58 loci and highlights GABAergic signaling

  2026cites this paper
• Genome-wide association study reveals the genetic basis of meat quality traits in Sichuan Shelduck.

  2026cites this paper
• Genetic risk and polygenic risk score assessment of prediabetes and progression to type 2 diabetes

  2025cites this paper
• Identification of genes associated with resistance trait to VPAHPND in Pacific white shrimp (Litopenaeus vannamei) using Bulk Segregation Analysis (BSA)

  2025cites this paper
• Mixture of common and uncommon pathways and genes regulating primary and secondary immunoglobulin M responses in chickens

  2025influential citation
• Genome-wide association study reveals the genetic basis of microelement concentration in cottonseed

  2025cites this paper
• Genome-wide association mapping for heat shock tolerance in Mercenaria mercenaria through SNP microarray analysis

  2025cites this paper
• Genome-wide association studies and genetic architecture of carcass traits in Angus beef cattle using imputed whole-genome sequences data

  2025cites this paper
• Genetic modifiers of somatic expansion and clinical phenotypes in Huntington’s disease highlight shared and tissue-specific effects

  2025cites this paper
• Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States

  2025influential citation
• Multi‐Experiment and Multi‐Locus Genome‐Wide Association Mapping for Grain Arsenic in Rice Population

  2025cites this paper
• Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F2 Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White

  2025influential citation
• Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs

  2025influential citation
• Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector

  2025cites this paper
• Genetic heterogeneity and homogeneity among orofacial cleft subtypes: genome-wide association studies in the cleft collective

  2025influential citation
• Identification of candidate genes for improving phosphorus use efficiency in a cowpea (Vigna unguiculata (L.) Walp.) multi-parent advanced generation inter-cross (MAGIC) population

  2025cites this paper
• Genetic markers associated with bone strength and density in Rhode Island Red laying hens

  2025cites this paper
• Genome-wide association study of seedling–plant resistance to stripe rust in bread wheat (Triticum aestivum L.) genotypes

  2025cites this paper
• Genetic structure of Ethiopian finger millet landraces and genome-wide association mapping for agronomic and nutritional traits

  2025cites this paper
• Genome wide population genetics and molecular surveillance of insecticide resistance in Anopheles stephensi mosquitoes from Awash Sebat Kilo in Ethiopia

  2025cites this paper
• Genome-Wide Association Study Reveals Candidate Genes Regulating Plant Height and First-Branch Height in Brassica napus

  2025influential citation
• A novel sex-associated genomic region in Catostomus fish species

  2025influential citation
• Temporal dynamics of color polymorphism and hybridization in Colias butterflies

  2025cites this paper
• Whole genome resequencing reveals genetic relationships and differences between three types of Hainan local pig breeds

  2025cites this paper
• Genomic Insights into a Highly Specific Marine Symbiosis Uncovers Geographic Structuring Without Co-Divergence Between Siphamia Cardinalfish and Their Bioluminescent Symbiont

  2025influential citation
• Dark side of the honeymoon: reconstructing the Asian x European rose breeding history through the lens of genomics

  2025cites this paper
• Screening of Adaptive Cultivars and Identification of QTNs Associated With Flowering Time and Related Traits of Diverse Soybean Cultivars Grown in Low-Latitude, High-Altitude Regions.

  2025cites this paper
• GWAS meta-analysis of CSF Alzheimer's disease biomarkers 18,948 individuals reveal novel loci and genes regulating lipid metabolism, brain volume and autophagy

  2025cites this paper
• Distinct patterns of cognitive traits in extreme old age and Alzheimer's disease

  2025cites this paper
• Genome wide association study of rice agronomical traits and seed ionome with the NARO Open Rice Collection.

  2025cites this paper
• Genome-wide association study (GWAS) provides insights into the genomic basis of reproduction-related traits in Chouardia litardierei (Asparagaceae)

  2025cites this paper
• Father’s adolescent body silhouette is associated with offspring asthma, lung function and BMI through DNA methylation

  2025cites this paper
• Discovering leaf and stripe rust resistance in soft red winter wheat through genome‐wide association studies

  2025influential citation
• Research on the mining of candidate genes for pepper fruit color and development of SNP markers based on SLAF-seq technology

  2025influential citation
• Dissecting the genetic architecture of key agronomic traits in lettuce using a MAGIC population

  2025cites this paper
• Unlocking the genetic code: a comprehensive Genome-Wide association study and gene set enrichment analysis of cell-mediated immunity in chickens

  2025influential citation
• Archipelago Method for Variant Set Association Test Statistics

  2025cites this paper
• A mechanistic basis for genetic assimilation in natural fly populations

  2025cites this paper
• Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq

  2025cites this paper
• Bivariate genome-wide association study reveals polygenic contributions to covariance between total carotenoid and dry matter contents in yellow-fleshed cassava (Manihot esculenta)

  2025cites this paper
• Unveiling the Potential Role of Dhurrin in Sorghum During Infection by the Head Smut Pathogen Sporisorium reilianum f. sp. reilianum

  2025influential citation
• Genome-wide genetic characterization and selection signatures in Anatolian Merino sheep

  2025influential citation
• Repeatable phenotypic but not genetic response to selection on body size in the black soldier fly

  2025cites this paper
• Fine mapping and identification of causal alleles at the Ur-11 locus controlling rust resistance in common bean (Phaseolus vulgaris L.)

  2025cites this paper
• Unraveling key genes and pathways involved in Verticillium wilt resistance by integrative GWAS and transcriptomic approaches in Upland cotton

  2025cites this paper
• Genome-Wide Association Study Reveals Single Nucleotide Polymorphisms Associated with Tail Length and Tail Kinks in Piglets

  2025influential citation
• Genetic risk factors for periodontitis: a genome-wide association study using UK Biobank data

  2025influential citation
• Whole genome sequencing identifies novel candidate genetic variants in canine stomatocytosis.

  2025cites this paper
• QTN detection and candidate gene identification for improved eating and cooking quality in rice using GWAS and PLS regression analysis

  2025cites this paper
• Exploring Predictive Modeling for Food Quality Enhancement: A Case Study on Wine

  2025cites this paper
• Aspergillus fumigatus mitogenomes and their influence on azole-resistant and -susceptible populations

  2025influential citation
• Pharmacogenomics of the Etonogestrel Contraceptive Implant

  2025cites this paper
• Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance

  2025cites this paper
• Bioenergetic-related gene expression in the hippocampus predicts internalizing vs. externalizing behavior in an animal model of temperament

  2025influential citation
• Investigation of selection signatures of dairy goats using whole-genome sequencing data

  2025cites this paper
• Genome-Wide Analysis of Genetic Predispositions Linked to Damaged Membranes and Impaired Fertility as Indicators of Compromised Sperm-Egg Interaction Mechanisms in Frozen-Thawed Rooster Semen.

  2025influential citation
• Identification of Elite Alleles and Candidate Genes for the Cotton Boll Opening Rate via a Genome-Wide Association Study

  2025influential citation
• Genetic Determinants Of Major Depressive Disorder (MDD) Among Adult Persons Living With HIV In Uganda

  2025cites this paper
• Tapping natures rhythm: the role of season in mitochondrial function and genetics in the UK biobank

  2025cites this paper
• Mechanistic Insights into Drug-Induced Guillain–Barré Syndrome: A Large-Cohort Analysis of the FAERS Database

  2025influential citation
• Genetic variants predisposing to an increased risk of kidney stone disease

  2025cites this paper
• Instrumenting Carotid Sonography Biomarkers and Polygenic Risk Score As a Novel Screening Approach for Retinal Detachment

  2025cites this paper
• Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat

  2025cites this paper
• The Relative Roles of Selection and Drift in the Chaffinch Radiation (Aves: Fringilla) Across the Atlantic Archipelagos of Macaronesia

  2025cites this paper
• Uncovering the genomic basis of phenological traits in Chouardia litardierei (Asparagaceae) through a genome-wide association study (GWAS)

  2025cites this paper
• Whole Genome Variable Number Tandem Repeat Analysis in Alzheimer Disease

  2025cites this paper