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In recent years, microRNAs (miRNAs) play critical roles in many important biological processes, and are therefore studied as key regulators of gene expression involved in complex diseases. On the other hand, the simultaneous genotyping of hundreds of thousands of single nucleotide polymorphisms (SNP) have provided an excellent chance for genome-wide association studies (GWAS). However, currently identified genetic variants collectively can explain only a small proportion of disease phenotypic variance. It is therefore suggested that functional SNPs or SNPs in microRNA genes or target sites might be important signals associated with human complex diseases. To explore disease-related microRNAs, we performed a genome-wide scan for WTCCC-CAD (coronary artery disease) SNP data, and extracted functional risk SNPs. By combining functional risk SNPs (genes) with differentially expressed microRNAs, we identified CAD-related microRNAs or microRNA clusters. Our method can help understanding miRNA function and disease, as well as in exploring the novel mechanism connecting miRNAs in the function.