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PAINTOR specifications


Unique identifier OMICS_11039
Alternative name Probabilistic Annotation INtegraTOR
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data PAINTOR takes as input the following data for each set of SNPs at a locus: (i) summary association statistics (Z-scores); linkage disequilibrium matrix/matrices (pairwise Pearson correlations coefficients between each SNP) and (iii) functional annotation matrix (binary indicator of annotation membership).
Output data The main output of PAINTOR is a probability for each variant to be causal that can be used for selection of SNPs to be tested for biological causality in functional assays.
Operating system Unix/Linux
Computer skills Advanced
Version 2.1
Stability Stable
Eigen, Nlopt
Source code URL
Maintained Yes


No version available


  • person_outline Bogdan Pasaniuc

Publications for Probabilistic Annotation INtegraTOR

PAINTOR citations


Determining Genetic Causal Variants Through Multivariate Regression Using Mixture Model Penalty

Front Genet
PMCID: 5844985
PMID: 29556250
DOI: 10.3389/fgene.2018.00077
call_split See protocol

[…] and intergenic SNPs (Schork et al., ). SNPs in the MHC region can be considered to be enriched when studying immune related diseases (Ellinghaus et al., ).Using existing packages such as CAVIAR, DAP, PAINTOR, RiVIERA, and S-LDSC (Finucane et al., ), one could obtain a quantitative assessment of the causal nature of individual SNPs. These results can be directly used as prior probabilities (π~1) in […]


Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease

Circ Res
PMCID: 5805277
PMID: 29212778
DOI: 10.1161/CIRCRESAHA.117.312086

[…] ry contribution of genetic variation, we used GARFIELD, analyzing the enrichment of genome-wide association summary statistics in tissue-specific functional elements at given significance thresholds. Probabilistic Annotation Integrator was used to fine-map loci by integrating genetic association signal strength with genomic functional annotation data. We explored the potential target genes of thes […]


Statistical methods to detect pleiotropy in human complex traits

Open Biol
PMCID: 5717338
PMID: 29093210
DOI: 10.1098/rsob.170125

[…] investigators built a revised approach, GPA-MDS, which combines multidimensional scaling with the GPA algorithm to draw visual representations of the relationships between multiple phenotypes [].FastPAINTOR, an extension to the single-trait fine-mapping algorithm PAINTOR [], additionally models the LD structure at a locus which can improve accuracy []. Following a similar model to GPA, a Bayesian […]


Trans ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL C GWAS Locus

PMCID: 5592946
PMID: 28754724
DOI: 10.1534/g3.117.300088
call_split See protocol

[…] To prioritize functional variants, we analyzed variants at the ANGPTL8 locus using both CAVIAR () and PAINTOR (). CAVIAR estimates the posterior probability of a variant being functional by jointly modeling the P-values and β association statistics, and PAINTOR leverages functional genomic annotation […]


Trans ethnic meta regression of genome wide association studies accounting for ancestry increases power for discovery and improves fine mapping resolution

Hum Mol Genet
PMCID: 5755684
PMID: 28911207
DOI: 10.1093/hmg/ddx280
call_split See protocol

[…] e) Bayes’ factors were used to obtain the posterior probability of driving the association for each variant across the locus. Finally, we undertook trans-ethnic meta-analysis across populations using PAINTOR (), assuming a single causal variant at the locus (option ‘-enumerate 1’), and approximating LD between variants in each population from haplotypes in the 1000 Genomes Project Phase 3 referenc […]


Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression

PMCID: 5555460
PMID: 28600440
DOI: 10.1534/g3.117.043752

[…] ants are generally not known, and there are no established methods for comprehensive screening transcriptome-wide for localization of multi-locus local eQTL effects. Two exhaustive search algorithms, PAINTOR () and CAVIARBF (), hold promise for detailed dissection of multisite models at individual loci, and a Bayesian shotgun stochastic search algorithm, FINEMAP (), has recently been proposed for […]


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PAINTOR institution(s)
Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
PAINTOR funding source(s)
This research was supported by NIH grants R01-HG006399, R01-GM53275, and R21-CA182821.

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