SNP to gene mapping (LDSeeker)

To facilitate snp to gene mapping, we developed a unified consensus reference integrating the GRCh38.p14 (GCF_000001405.40.gz) and GRCh37.p13 (GCF_000001405.25) genome assemblies. Genomic coordinates for each build were cross-referenced with their respective NCBI gene location maps (NCBI38 and NCBI37.3) to define gene boundaries, including a ±20kb flanking window to capture potential regulatory or near-gene intergenic variants. Variants falling within these flanking regions are explicitly denoted with an asterisk (*) to distinguish them from intronic or exonic mappings. The resulting reference provides an exhaustive consolidation of both assemblies, encompassing shared variants as well as those unique to a single build. By abstracting the complexities of coordinate lift-overs and assembly-specific references into a single, optimized Parquet-based architecture, this resource enables rapid post-GWAS processing—such as gene-based association studies and fine-mapping from summary statistics. This framework is integrated into a web-based utility, allowing researchers to perform robust gene-mapping without the need for custom scripts or manual genome-build reconciliation.为实现单核苷酸多态性（Single Nucleotide Polymorphism, SNP）到基因的定位分析，本研究构建了一套统一的整合参考集，纳入了GRCh38.p14（GCF_000001405.40.gz）与GRCh37.p13（GCF_000001405.25）两个版本的基因组组装序列。针对每个基因组组装版本，我们将其基因组坐标与对应版本的NCBI基因定位图谱（NCBI38与NCBI37.3）进行交叉参照，以此明确基因边界，并额外扩展±20kb的侧翼区域，以捕获潜在的调控变异或基因邻近的基因间区变异。位于上述侧翼区域的变异将通过星号（*）进行明确标注，以区别于内含子或外显子区域的定位结果。最终生成的参考集对两个基因组组装序列进行了全面整合，涵盖了二者共有的变异以及仅在单个组装版本中存在的特有变异。本资源将基因组坐标跨版本转换与特定组装版本参考序列带来的复杂操作封装至一套统一优化的基于Parquet格式的架构中，可支持全基因组关联研究（Genome-Wide Association Study, GWAS）后的快速分析流程，例如基于基因的关联分析以及从汇总统计数据中开展的精细定位研究。该框架已集成至一款网页端工具中，研究人员无需编写自定义脚本或手动协调不同基因组组装版本，即可开展可靠的基因定位分析。