Functional Analysis of a Carotid Intima-Media Thickness Locus Implicates <i>BCAR1</i> and Suggests a Causal Variant

<jats:sec> <jats:title>Background—</jats:title> <jats:p> Carotid intima-media thickness (IMT) is a marker of subclinical atherosclerosis that can predict cardiovascular disease events over traditional risk factors. This study examined the <jats:italic>BCAR1-CFDP1-TMEM170A</jats:italic> locus on chromosome 16, associated with carotid IMT and coronary artery disease in the IMT and IMT-Progression as Predictors of Vascular Events (IMPROVE) cohort, to identify the functional variant. </jats:p> </jats:sec> <jats:sec> <jats:title>Methods and Results—</jats:title> <jats:p> In analysis of the locus lead single nucleotide polymorphism (SNP; rs4888378, intronic in <jats:italic>CFDP1</jats:italic> ) in Progressione della Lesione Intimale Carotidea (PLIC), the protective AA genotype was associated with slower IMT progression in women ( <jats:italic>P</jats:italic> =0.04) but not in men. Meta-analysis of 5 cohort studies also supported a protective effect of the A allele on common carotid IMT in women only (women: β=−0.0047, <jats:italic>P</jats:italic> =1.63×10 <jats:sup>–4</jats:sup> ; men: β=−0.0029, <jats:italic>P</jats:italic> =0.0678). Two hundred fourteen noncoding variants in strong linkage disequilibrium ( <jats:italic>r</jats:italic> <jats:sup>2</jats:sup> ≥0.8) with rs4888378 were identified from 1000 Genome Project. ENCODE regulatory chromatin marks were used to create a shortlist of 6 possible regulatory variants. Electrophoretic mobility shift assays on the shortlist detected allele-specific protein binding to the lead SNP rs4888378; multiplexed competitor electrophoretic mobility shift assays implicated FOXA as the protein. Luciferase reporter assays on rs4888378 showed a significant 35% to 92% ( <jats:italic>P</jats:italic> =0.0057; <jats:italic>P</jats:italic> =4.0×10 <jats:sup>–22</jats:sup> ) decrease in gene expression with the A allele. Expression quantitative trait loci analysis confirmed previously reported associations of rs4888378 with <jats:italic>BCAR1</jats:italic> in vascular tissues. </jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions—</jats:title> <jats:p> Molecular studies suggest the lead SNP as a potentially causal SNP at the <jats:italic>BCAR1</jats:italic> - <jats:italic>CFDP1</jats:italic> - <jats:italic>TMEM170A</jats:italic> locus, and expression quantitative trait loci studies implicate <jats:italic>BCAR1</jats:italic> as the causal gene. This variant showed stronger effects on common carotid IMT in women, raising questions about the mechanism of the causal SNP on atherosclerosis. </jats:p> </jats:sec>