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SCAN database: facilitating integrative analyses of cytosine modification and expression QTL
Wei Zhang1, Eric R Gamazon2, Xu Zhang2
1Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA wei.zhang1@northwestern.edu.
The SCAN database now includes epigenetic modification data (mQTL) alongside genetic variant information (eQTL). This enhances functional annotation for understanding complex human traits and genetic variations.
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- Functional annotation of genetic variants like SNPs and CNVs is crucial for understanding complex human traits.
- Previous studies mapped expression quantitative trait loci (eQTL) in diverse populations.
- The SCAN database previously provided eQTL data from HapMap lymphoblastoid cell lines.
Purpose of the Study:
- To integrate comprehensive cytosine modification quantitative trait loci (mQTL) mapping results into the SCAN database.
- To enhance the SCAN database's functional genomic information by incorporating epigenetic data.
- To demonstrate the utility of the enhanced functional annotation system for genetic research.
Main Methods:
- Generated mQTL mapping results in HapMap CEU and YRI lymphoblastoid cell line (LCL) samples.
- Integrated these new mQTL data into the existing SCAN database.
- Evaluated the utility of the enhanced functional annotation system.
Main Results:
- The SCAN database now incorporates extensive mQTL data.
- The enhanced system provides a more comprehensive layer of functional genomic information.
- The integrated data facilitates a deeper understanding of genetic and epigenetic influences on complex traits.
Conclusions:
- Integrating mQTL data significantly enhances the functional annotation capabilities of the SCAN database.
- The improved SCAN database serves as a valuable resource for interpreting genetic variants and their role in human complex traits.
- This work highlights the importance of combining genetic and epigenetic information for a holistic view of gene regulation.
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