Thousands of human disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding genome, but only a handful have been demonstrated to affect gene expression and human biology. We computationally identified risk-associated SNPs in deeply conserved non-exonic elements (CNEs) potentially contributing to 45 human diseases. We further demonstrated that human CNE1/rs17421627 associated with retinal vasculature defects showed transcriptional activity in the zebrafish retina, while introducing the risk-associated allele completely abolished CNE1 enhancer activity. Furthermore, deletion of CNE1 led to retinal vasculature defects and to a specific downregulation of microRNA-9, rather than MEF2C as predicted by the original genome-wide association studies. Consistent with these results, miR-9 depletion affects retinal vasculature formation, demonstrating MIR-9-2 as a critical gene underpinning the associated trait. Importantly, we validated that other CNEs act as transcriptional enhancers that can be disrupted by conserved non-coding SNPs. This study uncovers disease-associated non-coding mutations that are deeply conserved, providing a path for in vivo testing to reveal their cis-regulated genes and biological roles.

中文翻译：

---

深入保存的非编码GWAS SNP的筛选揭示了 与人类视网膜脉管系统缺陷相关的 MIR-9-2功能突变

成千上万与人类疾病相关的单核苷酸多态性（SNP）位于非编码基因组中，但只有极少数被证明会影响基因表达和人类生物学。我们通过计算确定了高度保守的非外显子元素（CNE）中与风险相关的SNP，它们可能导致45种人类疾病。我们进一步证明，与视网膜脉管系统缺陷相关的人CNE1 / rs17421627在斑马鱼视网膜中显示出转录活性，同时引入了与风险相关的等位基因，从而完全废除了CNE1增强子活性。此外，CNE1的缺失导致视网膜脉管系统缺损，并导致microRNA-9而非MEF2C的特异性下调。如原始的全基因组关联研究所预测的那样。与这些结果一致，miR-9耗竭会影响视网膜脉管系统的形成，表明MIR-9-2是支撑相关性状的关键基因。重要的是，我们验证了其他CNE作为转录增强子，可以被保守的非编码SNP破坏。这项研究发现了与疾病相关的非编码突变，这些突变被高度保守，为体内测试揭示其顺式调控基因和生物学作用提供了一条途径。