ArticleDatabase : the journal of biological databases and curation2015
SCAN database: facilitating integrative analyses of cytosine modification and expression QTL.
Open access · goldAbstract readDataset
In one paragraph
Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18citing papers in PubMed
2.7field-weighted citation impact, top 9% of its field
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Who cites it
18 citing papers in PubMed, 22 citations in OpenAlex.
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- Common variants associated with changes in levels of circulating free fatty acids after administration of glucose-insulin-potassium (GIK) therapy in the IMMEDIATE trial.The pharmacogenomics journal · 2017Trial
- Endophenotype 2.0: updated definitions and criteria for endophenotypes of psychiatric disorders, incorporating new technologies and findings.Translational psychiatry · 2024Review
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- The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits.Cell metabolism · 2023Article
- PIK3R5 genetic predictors of hypertension induced by VEGF-pathway inhibitors.The pharmacogenomics journal · 2022Article
- Similar burden of pathogenic coding variants in exceptionally long-lived individuals and individuals without exceptional longevity.Aging cell · 2020Article
- Is Any Cardiovascular Disease-Specific DNA Methylation Biomarker Within Reach?Current atherosclerosis reports · 2020Review
- Cancer-specific expression quantitative loci are affected by expression dysregulation.Briefings in bioinformatics · 2020Article
- Genetic architecture of subcortical brain structures in 38,851 individuals.Nature genetics · 2019Article
- Genome-wide association study of maternal genetic effects and parent-of-origin effects on food allergy.Medicine · 2018Observational
- PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types.Nucleic acids research · 2018Article
- Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era.Genome biology · 2017Review
- Epigenetic contribution of the myosin light chain kinase gene to the risk for acute respiratory distress syndrome.Translational research : the journal of laboratory and clinical medicine · 2017Article
- Chronic Periodontitis Genome-wide Association Study in the Hispanic Community Health Study / Study of Latinos.Journal of dental research · 2017Article
- Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines.Human genetics · 2016Article
- The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.American journal of human genetics · 2015Article
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Authors and funding
8 authors at 4 institutions in 2 countries.
Wei ZhangDepartment 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.
Eric R GamazonDepartment 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.
Xu ZhangDepartment 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.
Anuar KonkashbaevDepartment 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.
Cong LiuDepartment 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.
Keely L SzilágyiDepartment 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.
M Eileen DolanDepartment 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 CoxDepartment 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.
University of Chicago · USUniversity of Illinois Chicago · USNingbo University · CNNorthwestern University · US
Funding
Whole GenomeU01GM061393 · NIGMS · UNIVERSITY OF CHICAGO · PI RATAIN, MARK J · 2000 to 2014
$39.0MTRANSGENIC COREP60DK020595 · NIDDK · UNIVERSITY OF CHICAGO · PI BELL, GRAEME I · 1985 to 2012
$25.5MPilot and Feasibility ProgramP30DK020595 · NIDDK · UNIVERSITY OF CHICAGO · PI Raghavendra G Mirmira · 2013 to 2026
$20.9MRe-Engineering Translational Research at the University of ChicagoUL1TR000430 · NCATS · UNIVERSITY OF CHICAGO · PI SOLWAY, JULIAN · 2012 to 2016
$20.2MVariation in Hormone and xenobiotic metabolizing enzyme genes and breast cancerP50CA125183 · NCI · UNIVERSITY OF CHICAGO · PI COX, NANCY · 2006 to 2010
$11.3MHarnessing GTEx to Create Transcriptome Knowledge and Inform Disease BiologyR01MH101820 · NIMH · UNIVERSITY OF CHICAGO · PI COX, NANCY J, NICOLAE, DAN LIVIU · 2013 to 2015
$2.3MGenome-wide Association Mapping of Metabolic, Lung and Cardiovascular PhenotypesU01HL084715 · NHLBI · UNIVERSITY OF CHICAGO · PI COX, NANCY J · 2006 to 2008
$836kUsing the Transcriptome for SNP and Gene AnnotationR01MH090937 · NIMH · UNIVERSITY OF CHICAGO · PI COX, NANCY J, NICOLAE, DAN LIVIU · 2010 to 2012
$825kEpigenetic and Genetic Dissection of Drug ResponseR21HG006367 · NHGRI · UNIVERSITY OF ILLINOIS AT CHICAGO · PI DOLAN, MARY EILEEN, GODLEY, LUCY ANN · 2011 to 2012
$462kNCATS NIH HHS UL1 TR000430NCI NIH HHS P50 CA125183NHGRI NIH HHS R21 HG006367NHLBI NIH HHS U01 HL084715NIDDK NIH HHS P30 DK020595NIDDK NIH HHS P60 DK020595NIDDK NIH HHS P60 DK20595NIGMS NIH HHS U01 GM061393NIGMS NIH HHS U01 GM61393NIMH NIH HHS R01 MH090937NIMH NIH HHS R01 MH101820
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.
Indexed as
CytosineDatabases, Nucleic AcidGene Expression RegulationPolymorphism, Single NucleotideQuantitative Trait LociTranscriptomeBlack PeopleHumansWhite PeopleCytosine
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