atSNP Search provides statistical evaluation of impact of SNPs on transcription factor-DNA interactions based on position weight matrices (PWMs). The current version is built on SNPs from dbSNP Build 144 for the human genome assembly GRCh38/hg38. atSNP Search uses in silico calculations based on the statistical method in Zuo et al., Bioinformatics (2015). atSNP first-time users can start scanning vast amounts of SNP-PWM combinations for potential gain and loss of function with two key features:

  • p-values quantifying the impact of SNP on the PWM matches (p-value SNP impact)
  • composite logo plots.

atSNP identifies and quantifies best DNA sequence matches to the transcription factor PWMs with both the reference and the SNP alleles in a small window around the SNP location (up to +/- 30 base pairs and considering subsequences spanning the SNP position). It evaluates statistical significance of the match scores with each allele and calculates statistical significance of the score difference between the best matches with the reference and SNP alleles.

The discovery of best matches with the reference and SNP alleles are conducted separately. As a result, genomic subsequences providing the best match with each allele may be different. The change in goodness of match with the reference and SNP alleles alleles indicates in silico impact of SNPs on transcription factor binding ability to DNA. atSNP Search also provides a composite logo plot for easy visualization of the quality of the reference and SNP allele matches to the PWM and the influence of SNPs on the change in match. Read more under "Help".

News and Updates

atSNP Search human version 1.0.0 has been released on January 1st, 2018.

The current version of atSNP Search evaluated 133 million SNPs from the NCBI database of genetic variation (dbSNP Build 144 for human genome GRCh38) with 2,270 PWMs (position weight matrices) from two major sources of transcription factor position weight matrix libraries. These are the JASPAR and ENCODE libraries. atSNP Search evaluated 307 billion SNP-PWM pairs. The current release enables querying of these statistical evaluations which exhibit a significant score change or a significant match with either the reference or the SNP allele. As a result, 37 billion SNP-PWM pairs with p-value SNP impact, p-value Reference, and/or p-value SNP less than or equal to 0.05 are currently available to query.


If you have any questions concerning atSNP Search, please post your question publicly in the atSNP User Group. For other questions or concerns you may send email to


This site is supported by:

Center for Predictive Computational Phenotyping
University of Wisconsin - Madison

National Institutes of Health - Big Data to Knowledge (BD2K)
Initiative under Award Number U54 AI117924