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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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rSNPBase: a database for curated regulatory SNPs.

Liyuan Guo1, Yang Du, Suhua Chang

  • 1Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing 100101, China and University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.

Nucleic Acids Research
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Summary
This summary is machine-generated.

rSNPBase is a new database offering reliable regulatory SNP annotations using experimental data. It helps researchers identify regulatory SNPs (rSNPs) and their associated genes for complex trait studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Human regulatory single nucleotide polymorphisms (rSNPs) are crucial for understanding gene regulation.
  • Existing SNP annotation databases lack comprehensive and experimentally validated regulatory information.

Purpose of the Study:

  • To introduce rSNPBase, a curated database of human rSNPs with experimentally supported regulatory features.
  • To provide a user-friendly resource for analyzing SNP regulatory functions and identifying candidate SNPs for genetic studies.

Main Methods:

  • Annotation of all human SNPs against experimentally validated regulatory elements.
  • Analysis of proximal, distal transcriptional, and post-transcriptional regulation.
  • Inclusion of linkage disequilibrium (LD) analysis for SNP-sets and incorporation of spatio-temporal and eQTL data.

Main Results:

  • rSNPBase offers reliable annotations based on experimental evidence.
  • The database covers diverse regulatory mechanisms and identifies potentially regulated genes.
  • It annotates regulatory features to SNP-sets considering LD, enhancing analysis scope.

Conclusions:

  • rSNPBase provides a comprehensive and reliable resource for regulatory SNP annotation.
  • The database facilitates the selection of candidate SNPs for further genetic research.
  • It aids in exploring causal SNPs and understanding complex phenotype mechanisms.