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3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes.

Yiming Lu1, Cheng Quan1, Hebing Chen2

  • 1Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China.

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|October 30, 2016
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Summary

3DSNP is a new database that annotates human noncoding variants by analyzing their roles in gene regulation through three-dimensional (3D) chromatin looping. It helps researchers understand how these variants impact clinical phenotypes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The human genome's noncoding regions contain functional elements and disease-associated regulatory variants.
  • Three-dimensional (3D) chromatin looping mediates interactions between regulatory elements and distal target genes.

Purpose of the Study:

  • To present 3DSNP, an integrated database for annotating human noncoding variants.
  • To explore the role of noncoding variants in distal gene regulation via 3D chromatin interactions.

Main Methods:

  • Integration of 3D chromatin interaction data, cell-type-specific local chromatin signatures, and linkage disequilibrium (LD) information from the 1000 Genomes Project.
  • Development of visualization tools for integrated chromatin signatures and variant associations.
  • Implementation of a scoring system to quantify SNP functionality.

Main Results:

  • 3DSNP provides comprehensive annotation of human noncoding variants.
  • The database integrates diverse functional data to assess variant impact.
  • Visualization tools facilitate the exploration of complex genomic interactions.

Conclusions:

  • 3DSNP is a valuable resource for annotating the human noncoding genome.
  • It aids in investigating the impact of noncoding variants on clinical phenotypes.
  • The database facilitates the selection of functionally significant variants from large datasets.