Genome-wide association studies (GWAS) have identified hundreds of primarily non-coding disease-susceptibility variants that further need functional interpretation to prioritize and discriminate the disease-relevant variants. We present a comprehensive genome-wide non-coding variant prioritization scheme followed by validation using Pyrosequencing and TaqMan assays in asthma. We implemented a composite Functional Annotation Score (cFAS) to investigate over 32,000 variants consisting of 1525 GWAS-lead asthma-susceptibility variants and their LD proxies (r² ≥ 0.80). Functional annotation pipeline in cFAS revealed 274 variants with significant score at 1% false discovery rate. This study implicates a novel locus 4p16 (SLC26A1) with eQTL variant (rs11936407) and known loci in 17q12-21 and 5q22 which encode ORM1-like protein 3 (ORMDL3, rs406527, and rs12936231) and thymic stromal lymphopoietin (TSLP, rs3806932 and rs10073816) epithelial gene, respectively. Follow-up validation analysis through pyrosequencing of CpG sites in and nearby rs4065275 and rs11936407 showed genotype-dependent hypomethylation on asthma cases compared with healthy controls. Prioritized variants are enriched for asthma-specific histone modification associated with active chromatin (H3K4me1 and H3K27ac) in T cells, B cells, lung, and immune-related interferon gamma signaling pathways. Our findings, together with those from prior studies, suggest that SNPs can affect asthma by regulating enhancer activity, and our comprehensive bioinformatics and functional analysis could lead to biological insights into asthma pathogenesis.

Graphic abstract

全基因组关联研究 (GWAS) 已经确定了数百种主要的非编码疾病易感性变异，这些变异进一步需要功能解释来优先考虑和区分疾病相关变异。我们提出了一个全面的全基因组非编码变异优先方案，然后在哮喘中使用焦磷酸测序和 TaqMan 检测进行验证。我们实施了一个复合功能注释评分 (cFAS) 来研究超过 32,000 种变异，其中包括 1525 GWAS 主导的哮喘易感变异及其 LD 代理 ( r ² ≥ 0.80)。cFAS 中的功能注释管道揭示了 274 个变体，在 1% 的错误发现率下得分很高。本研究涉及具有 eQTL 变体 (rs11936407) 的新基因座 4p16 (SLC26A1) 和 17q12-21 和 5q22 中的已知基因座，这些基因座编码 ORM1 样蛋白 3（ORMDL3、rs406527 和 rs12936230rs129362318 和 rs129362231 和 rs1293623231 和 rs129362310 thyrs13010 ) 上皮基因，分别。通过对 rs4065275 和 rs11936407 及其附近的 CpG 位点进行焦磷酸测序的后续验证分析显示，与健康对照相比，哮喘病例存在基因型依赖性低甲基化。优先变体富含与 T 细胞、B 细胞、肺和免疫相关干扰素 γ 信号通路中活性染色质（H3K4me1 和 H3K27ac）相关的哮喘特异性组蛋白修饰。我们的发现，

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