SCAN database: facilitating integrative analyses of cytosine modification and expression QTL
Year: 2015
Type: article
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.
Source: Database
Authors: W. Zhang, E. R. Gamazon, X. Zhang, A. Konkashbaev, C. Liu, K. L. Szilagyi, M. E. Dolan, N. J. Cox
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,729
Funders: University of Chicago, National Institutes of Health, National Heart, Lung, and Blood Institute, National Institute of Mental Health, National Human Genome Research Institute, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Diabetes and Digestive and Kidney Diseases, National Center for Advancing Translational Sciences
Awards: G1756836520, G2021055342, Using the Transcriptome for SNP and Gene Annotation, G2807054497, G3389740441, Re-Engineering Translational Research at the University of Chicago, G4277768125, Harnessing GTEx to Create Transcriptome Knowledge and Inform Disease Biology, Epigenetic and Genetic Dissection of Drug Response, G634178657, Genome-wide Association Mapping of Metabolic, Lung and Cardiovascular Phenotypes, PAAR-Pharmacogenomics of Anticancer Agents Research Group, SPORE in Breast Cancer, Diabetes Research and Training Center, G8810271873, G8880508232, Diabetes Research and Training Center
OpenAlex ID: W2165696350