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SCAN database: facilitating integrative analyses of cytosine modification and expression QTL.

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journal contribution
posted on 29.01.2016 by W. Zhang, ER Gamazon, X. Zhang, A. Konkashbaev, C. Liu, KL Szilágyi, ME Dolan, NJ Cox
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.




National Human Genome Research Institute (R21 HG006367 to W.Z. and M.E.D.); National Institute of General Medical Sciences (U01 GM61393 to M.E.D. and N.J.C.); National Institute of Mental Health (R01 MH090937 to N.J.C.); the ENDGAMe (ENhancing Development of Genome-wide Association Methods); National Heart, Lung, and Blood Institute (U01 HL084715 to N.J.C.); Center for Neuropsychiatric Genetics and Molecular Neuroscience at the University of Chicago; The University of Chicago DRTC (Diabetes Research and Training Center) by the National Institute of Diabetes and Digestive and Kidney Diseases (P60 DK20595); The University of Chicago Breast Cancer SPORE by the National Cancer Institute (P50 CA125183). Funding for open access charge: R21 HG006367


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This is the copy of an article published in Database © 2015 Oxford University Press Publications.


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