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.