Disease Markers

Research Article

A Novel Polymorphism in the Promoter of the CYP4A11 Gene Is Associated with Susceptibility to Coronary Artery Disease

Table 6

Bioinformatic analysis for the regulatory potential of the studied SNPs.

SNP

Allele

Location

SNP Function Prediction (FuncPred)¹

Regulatory annotations on SNPs (rSNPBase)²

Transcription factors potentially related with SNP

TFBS

miRNA

Regulatory potential

rSNP

LD-proxy of rSNP (r² > 0.8)

Proximal regulation

Distal regulation

miRNA regulation

RNA binding protein- mediated regulation

eQTL

TRANSFAC database

rSNPBase

rs3890011

C/G

Intron

Yes

—

rs9332978

T/C

Promoter

Yes

AIRE, ATF6, CDPCR3, CEBPA, CEBPDELTA, CEBPGAMMA, CEBP, CRX, FAC1, GRE, IPF1, MYOGNF1, OCT1, OCT4, OCT, PAX3, PAX6, PAX8, PLZF, POU3F2, PPARG, S8, SP3, SREBP1, SREBP, TAXCREB, ZF5

FOXA1, HNF4A, ARID3A, CEBPB

rs9333029

A/G

Intron

Yes

—

rs3093098

A/G

Intron

Yes

AP4, CACD, DR4, ETF, GABP, GRE, HAND1E47, HIC1, MYOGNF1, PAX3, PLZF, PPARA, RFX, SP1, SP3, SPZ1, SZF11, TAXCREB, TBX5, TEL2, VDR, WT1, ZF5

Pol2

rs1558139

G/A

Intron

Yes

—

Data predicted by the SNP Function Prediction tool, National Institute of Environmental Health Sciences (https://snpinfo.niehs.nih.gov/snpinfo/). TFBS: transcription factor binding site; ND: no data. Data obtained at rSNPBase, a database of curated regulatory SNPs (http://rsnp.psych.ac.cn). rSNP, rSNPBase identified regulatory SNPs; LD-proxy of rSNP (r² > 0.8), SNP in strong LD with rSNPs; proximal regulation, SNP involved in proximal transcriptional regulation; distal regulation, SNP involved in distal transcriptional regulation; miRNA regulation, SNP within mature miRNA; RNA binding protein mediated regulation, SNP involved in RNA binding protein-mediated post-transcriptional regulation; eQTL, SNP with experimental eQTL evidence. TRANSFAC is the database on potential transcription factor recognition sites (BIOBASE Corporation, Wolfenbuettel, Germany).