geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome
MetadataShow full item record
AuthorGómez Martín, Cristina; Aparicio Puerta, Ernesto; Medina, J. M.; Barturen, Guillermo; Oliver Jiménez, José L.; Hackenberg, Michael
SNPsDNA methylationGene regulation
C. Gómez-Martín, E. Aparicio-Puerta, J.M. Medina, Guillermo Barturen, J.L. Oliver, M. Hackenberg, geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome, Journal of Molecular Biology, Volume 433, Issue 11, 2021, 166709, ISSN 0022-2836, [https://doi.org/10.1016/j.jmb.2020.11.008]
SponsorshipSpanish Government European Commission AGL2017-88702-C2-2-R; Instituto de Salud Carlos III European Commission IFI16/00041
Genetic variation, gene expression and DNA methylation influence each other in a complex way. To study the impact of sequence variation and DNA methylation on gene expression, we generated geno(5)mC, a database that contains statistically significant SNP-CpG associations that are biologically classified either through co-localization with known regulatory regions (promoters and enhancers), or through known correlations with the expression levels of nearby genes. The SNP rs727563 can be used to illustrate the usefulness of this approach. This SNP has been associated with inflammatory bowel disease through GWAS, but it is not located near any gene related to this phenotype. However, geno5mC reveals that rs727563 is associated with the methylation state of several CpGs located in promoter regions of genes reported to be involved in inflammatory processes. This case exemplifies how geno5mC can be used to infer relevant and previously unknown interactions between described disease-associated SNPs and their functional targets.