Genetic Variants Allelic TF Binding Database

Searching for SNPs with differential Transcription factors (TF) binding.


GVAT database

This database characterizes the allelic binding of 95,886 common human single nucleotide polymorphisms (SNPs, MAF>1% in Eeuropean and Asian populations) to 270 distinct transcription factors (TFs). The SNPs were chosen from neighboring regions (<=500 kb) of 83 risk loci of type 2 diabetes (T2D) that were identified in several genome wide association studies (GWAS). The data were generated using SNP-SELEX.

For SNPs that are not included in the SNP-SELEX experiments, we also built deltaSVM models for 94 TFs that can be used to predict allelic TF binding to any SNPs.

For detail about the SNP selection and experimental or computational pipeline, please refer to the paper under review, “Systematic Analysis of Differential Transcription Factor Binding to Non-Coding Variants in the Human Genome.”.

The work has been supported by the National Institute of Health (NIH), Ludwig Institute of Cancer Research and the Swedish Research Council. We declare no conflict of interest.

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What's New

release undate

Version 1.3 released -- 01-13-2021
Version 1.2 released with updated deltaSVM models -- 09-06-2019
Version 1.1 released -- 05-04-2018
Version 1.0 released -- 12-25-2017


Jian Yan*, Yunjiang Qiu*, André M. Ribeiro dos Santos*, Yimeng Yin, Yang E. Li, Nick Vinckier, Naoki Nariai, Paola Benaglio, Anugraha Raman, Xiaoyu Li, Shicai Fan, Joshua Chiou, Fulin Chen, Kelly A. Frazer, Kyle J. Gaulton, Maike Sander, Jussi Taipale, Bing Ren#.
Systematic analysis of binding of transcription factors to noncoding variants.
Nature. 2021
(*equal contribution.)