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

Zhang W, Gamazon ER, Zhang X, Konkashbaev A, Liu C, Szilágyi KL, Dolan ME, Cox NJ
Database (Oxford). 2015 2015

PMID: 25818895 · PMCID: PMC4375357 · DOI:10.1093/database/bav025

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.

© The Author(s) 2015. Published by Oxford University Press.

MeSH Terms (9)

African Continental Ancestry Group Cytosine Databases, Nucleic Acid European Continental Ancestry Group Gene Expression Regulation Humans Polymorphism, Single Nucleotide Quantitative Trait Loci Transcriptome

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