Integrative functional analysis of super enhancer SNPs for coronary artery disease

Journal of Human Genetics
Juexiao GongChunping Zeng

Abstract

Clinical research in coronary artery disease (CAD) primarily focused on genetic variants located in protein-coding regions. Recently, mutations fall within non-coding regions have been suggested to be essential to the pathogenesis of human complex disease. Super enhancer is a densely spaced cluster of transcriptional enhancers located in non-coding regions, which is critical for regulating cell-type specific gene expression. However, the underlying mechanism of the super enhancer single-nucleotide polymorphisms (SNPs) affecting the risk of CAD remains unclear. By integrating genome-wide association study (GWAS) meta-analysis of CAD and cell/tissue-specific histone modification data set, we identified 366 potential CAD-associated super enhancer SNPs in 67 loci, including 94 SNPs that are involved in regulating chromatin interactive and/or affecting the transcription factors binding affinity. Interestingly, we found 7 novel functional loci (CBFA2T3, ZMIZ1, DIP2B, SCNN1D/ACAP3, TMEM105, CAMK2G, and MAPK1) that CAD-associated super enhancer SNPs were clustered into the same or neighboring super enhancers. Pathway analysis showed a significant enrichment in several well-known signaling and regulatory processes, e.g., cAMP signaling ...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Nov 14, 2000·Arteriosclerosis, Thrombosis, and Vascular Biology·Y ZhuM B Stemerman
Aug 17, 2001·Current Opinion in Lipidology·S KinlayP Ganz
Aug 26, 2003·The American Journal of Pathology·Stefan GattenlöhnerAlexander Marx
May 13, 2004·JAMA : the Journal of the American Medical Association·Donald M Lloyd-JonesChristopher J O'Donnell
Jul 23, 2004·Thrombosis and Haemostasis·Axel SchlittHans J Rupprecht
Jul 28, 2004·Cardiovascular Research·Tong Zhang, Joan Heller Brown
Sep 15, 2005·Heart·D TousoulisC Stefanadis
Nov 30, 2006·PLoS Medicine·Colin D Mathers, Dejan Loncar
Apr 26, 2008·Trends in Cardiovascular Medicine·Haruhiro TokoIssei Komuro
Aug 22, 2008·Postgraduate Medical Journal·D TousoulisC Stefanadis
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 1, 2008·Bioinformatics·Andrew D JohnsonPaul I W de Bakker
May 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lucia A HindorffTeri A Manolio
Jun 17, 2009·Archives of Dermatology·Srjdan ProdanovichDaniel G Federman
Aug 3, 2010·Heart Rhythm : the Official Journal of the Heart Rhythm Society·Peter J Mohler, Thomas J Hund
Oct 12, 2010·Seminars in Cell & Developmental Biology·Pablo Sanchez-Soria, Todd D Camenisch
Feb 8, 2011·Cell·Michael Bulger, Mark Groudine
May 24, 2011·Journal of Dermatological Science·April W ArmstrongJohn C Rutledge
Jun 30, 2011·Menopause : the Journal of the North American Menopause Society·Katerina SaltikiMaria Alevizaki
Apr 28, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Monika S KowalczykDouglas R Higgs
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Sep 18, 2012·American Journal of Physiology. Lung Cellular and Molecular Physiology·Hong-Long JiSadis Matalon
Dec 4, 2012·Nature Genetics·Panos DeloukasNilesh J Samani
Feb 12, 2013·Briefings in Bioinformatics·Abu Z Dayem UllahClaude Chelala
Aug 27, 2013·Journal of the American College of Cardiology·Angie GhattasEduard Shantsila
Aug 31, 2013·Annual Review of Physiology·Gregg L Semenza
Oct 15, 2013·Cell·Denes HniszRichard A Young
Mar 26, 2014·Nature Reviews. Cardiology·Nathan D Wong
Aug 19, 2014·Trends in Biochemical Sciences·Matthew SlatteryRemo Rohs
Oct 30, 2014·Nucleic Acids Research·Damian SzklarczykChristian von Mering

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Citations

Jul 29, 2020·Frontiers in Genetics·Zhu TianZhiyun Wang
Nov 7, 2020·International Journal of Molecular Sciences·Rajiv Kumar SahYaowu Zheng
Jun 25, 2021·Scientific Reports·Allison Lesher WilliamsRalph V Shohet
Jul 3, 2021·International Journal of Molecular Sciences·Arina O DegtyarevaTatiana I Merkulova

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Methods Mentioned

BETA
ChIP-seq
genotyping
transgenic

Software Mentioned

SNPnexus
MACS
GWAS3D
WebGestalt
haploReg
SNP2TFBS
Gene Set Enrichment Analysis ( GSEA )
STRING
Bowtie

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