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Open Access Highly Accessed Research article

The distribution of SNPs in human gene regulatory regions

Yongjian Guo12 and D Curtis Jamison1*

Author Affiliations

1 School of Computational Sciences, George Mason University, Manassas, VA 20110 USA

2 Virginia Bioinformatics Institute, Bioinformatics Facility I (0477), Virginia Tech, Blacksburg, VA 24060 USA

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BMC Genomics 2005, 6:140  doi:10.1186/1471-2164-6-140

Published: 6 October 2005

Abstract

Background

As a result of high-throughput genotyping methods, millions of human genetic variants have been reported in recent years. To efficiently identify those with significant biological functions, a practical strategy is to concentrate on variants located in important sequence regions such as gene regulatory regions.

Results

Analysis of the most common type of variant, single nucleotide polymorphisms (SNPs), shows that in gene promoter regions more SNPs occur in close proximity to transcriptional start sites than in regions further upstream, and a disproportionate number of those SNPs represent nucleotide transversions. Additionally, the number of SNPs found in the predicted transcription factor binding sites is higher than in non-binding site sequences.

Conclusion

Current information about transcription factor binding site sequence patterns may not be exhaustive, and SNPs may be actively involved in influencing gene expression by affecting the transcription factor binding sites.