title: SCAN database: facilitating integrative analyses of cytosine modification and expression QTL.
abstract: Functional annotation of genetic variants including single nucleotide polymorphisms (SNPs) and copy number variations (CNV) promises to greatly improve our understanding of human complex traits. Previous transcriptomic studies involving individuals from different global populations have investigated the genetic architecture of gene expression variation by mapping expression quantitative trait loci (eQTL). Functional interpretation of genome-wide association studies (GWAS) has identified enrichment of eQTL in top signals from GWAS of human complex traits. The SCAN (SNP and CNV Annotation) database was developed as a web-based resource of genetical genomic studies including eQTL detected in the HapMap lymphoblastoid cell line samples derived from apparently healthy individuals of European and African ancestry. Considering the critical roles of epigenetic gene regulation, cytosine modification quantitative trait loci (mQTL) are expected to add a crucial layer of annotation to existing functional genomic information. Here, we describe the new features of the SCAN database that integrate comprehensive mQTL mapping results generated in the HapMap CEU (Caucasian residents from Utah, USA) and YRI (Yoruba people from Ibadan, Nigeria) LCL samples and demonstrate the utility of the enhanced functional annotation system.
authors.affiliation: 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 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.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: 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 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.
authors.forename: Eric R
authors.initials: ER
authors.lastname: Gamazon
authors.affiliation: 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 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.
authors.forename: Xu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Anuar
authors.initials: A
authors.lastname: Konkashbaev
authors.affiliation: 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.
authors.forename: Cong
authors.initials: C
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Keely L
authors.initials: KL
authors.lastname: Szilágyi
authors.affiliation: 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.
authors.forename: M Eileen
authors.initials: ME
authors.lastname: Dolan
authors.affiliation: 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 nancy.j.cox@vanderbilt.edu.
authors.forename: Nancy J
authors.initials: NJ
authors.lastname: Cox
mesh_terms: D044383:Black People; D003596:Cytosine; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D059467:Transcriptome; D044465:White People
chemical_list: D003596:Cytosine
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