SNP2TFBS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SNP2TFBS

Tool usage distribution map

This map represents all the scientific publications referring to SNP2TFBS per scientific context
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Associated diseases

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SNP2TFBS specifications


Unique identifier OMICS_28871
Interface Web user interface
Restrictions to use None
Input data A rsID code, a SNP set or a motif.
Input format VCF, BED
Output data A or some TF(s) with score difference or variability plots or a model.
Output format BED,TSV
Computer skills Basic
Stability Stable
Maintained Yes


  • PWNViewer
  • SNPViewer
  • SNSelect

SNP2TFBS citations


Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice

BMC Genomics
PMCID: 5923191
PMID: 29703142
DOI: 10.1186/s12864-018-4667-0

[…] 17.Ensembl genome browser. Accessed 15 Jun 2017.IMPC | International Mouse Phenotyping Consortium. Accessed 15 Jun 2017.Sanger Mouse SnpViewer. Accessed 15 Jun 2017.MGI-Mouse Genome Informatics-The international database resource for the laboratory mouse. http://www.informati […]


Integrative analysis of super enhancer SNPs for type 2 diabetes

PLoS One
PMCID: 5792005
PMID: 29385209
DOI: 10.1371/journal.pone.0192105

[…] ly predicted regulation features, therefore the model and algorithm selection is critical for this kind of analysis. For example, the reliability of the transcription factor binding site predicted by SNP2TFBS is a function of the accuracy of the PWM model which is less accurate than recently proposed approaches []. Further, genomic sequence with higher affinity to a transcription factor is often i […]


Single‐nucleotide polymorphism discovery and panel characterization in the African forest elephant

Ecol Evol
PMCID: 5817121
PMID: 29468037
DOI: 10.1002/ece3.3854

[…] or automatic allele calling usually result in a high proportion of unassigned genotype calls (Semagn, Babu, Hearne, & Olsen, ). Therefore, the genotype plots of each assay were visually checked using SNPviewer 2 software (LGC Genomics) and rescored manually if individuals that clearly belonged to a cluster had not been called automatically. The proportions of manually rescored genotypes and missin […]


COMT genotype and non recovery after a whiplash injury in a Northern European population

PMCID: 5709856
PMID: 29195501
DOI: 10.1186/s12891-017-1810-z
call_split See protocol

[…] petitive allele-specific PCR (KASPar) assay (KBioscience®), based on a public genome sequence (, was used to analyse the SNPs rs6269, rs4633 and rs4818. Alleles were determined using SNPviewer2®. χ2 test or Fisher’s test was used to investigate deviations from Hardy-Weinberg Equilibrium (HWE). The EM algorithm was computed using SNP & Variation Suite 7 (Golden Helix) to estimate l […]


Genome wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus

Nat Commun
PMCID: 5688097
PMID: 29142228
DOI: 10.1038/s41467-017-01818-4

[…] notations for the Roadmap ChromHMM 15-states and relevant histone marks. We implemented predictions of potentially regulatory effects of QTL-SNPs due to genetic variation of TFBS affinities using the SNP2TFBS database. In total, 857 cis-meQTL-SNPs and 44 cis-eQTL-SNPs with CADD-scores >5 were predicted to alter TFBSs (Supplementary Datas  and ). Consistent with an enrichment of cis-meQTL-CpGs in t […]


Congenital Cataract in Gpr161vl/vl Mice Is Modified by Proximal Chromosome 15

PLoS One
PMCID: 5279759
PMID: 28135291
DOI: 10.1371/journal.pone.0170724

[…] titute has used next-generation sequencing to sequence key laboratory mouse strains including C3H/HeJ and MOLF/EiJ, and the data were uploaded to a query website ( For identification of coding genetic variants, the minimal cataract modifying interval (Chr15: 13062568–28269407) as determined by subcongenic analysis was searched in the query s […]

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