PAINTOR: integration of functional and association data in fine-mapping studies

Finding causal variants that underlie known risk loci is one of the main post-GWAS challenges. Here we present PAINTOR (Probabilistic Annotation INtegraTOR), a probabilistic framework that integrates association strength with genomic functional annotation data to improve accuracy in selecting plausible causal variants for functional validation. The main output of PAINTOR are probabilities for every variant to be causal that can be used for prioritization in functional assays to establish biological causality.


  • PAINTOR 3.0 that incorporates multi-ethnic, multi-trait together with important sampling for improved computational speed can be downloaded here.
  • If your data is not imputed to the latest 1000Genomes (or other updated reference panel), we recommend doing so either from individual data or directly from summary association statistics (see ImpG-Summary).

Manuscripts describing PAINTOR:

Please contact Gleb ( or Bogdan ( for any comments or suggestions related to the software.

The software is free for non-commercial use, and may be licensed for commercial use.


This web-site is based upon work supported by the National Institutes of Health under awards R03 CA162200 and R01 GM053275. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funding agencies above.