dbTEvariant: A comprehensive human transposable element variant database

Transposable elements (TEs) constitute nearly half of the human genome and have profoundly influenced genome evolution, diversity, and function. Although most TE copies are ancient and inactive, a subset including LINE1, Alu, SVA, and HERVK remain capable of transposition and contribute to ongoing genomic variation. These active elements can alter gene expression, mediate chromosomal rearrangements, and influence disease susceptibility. Because recent insertions differ among individuals, many of their effects are polymorphic, highlighting the importance of identifying and cataloging polymorphic TE insertions to understand human genetic diversity. This thesis presents dbTEvariant, a comprehensive database of human transposable element variants. The database integrates TE insertion data from multiple large-scale genomic studies published between 2015 and 2025, harmonizing them through rigorous data standardization, coordinate alignment, and redundancy removal. Merging threshold was empirically determined using high-confidence long-read TE calls from the Human Pangenome Reference Consortium (HPRC) as a benchmark. The merged dataset provides a unified, non-redundant collection of TE variants across major human populations. The database supports TE visualization, filtering, and batch queries through a web interface implemented in React.js, with integrated IGV for locus-level inspection. By systematically consolidating polymorphic TE data across different studies, sequencing technologies dbTEvariant serves as a valuable resource for investigating TE-driven genetic variation.