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 pathway and ErbB signaling pathway, which play a key role in CAD metabolism. Our results highlight the potential functional importance of CAD-associated super enhancer SNPs and provide the targets for further insights on the pathogenesis of CAD.