3DSNP

3DSNP annotates noncoding single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) by linking them to three-dimensional chromatin interactions to infer regulatory impacts on gene expression and disease mechanisms.

Key Features:

• Integration of long-read sequencing and single-cell technologies: Incorporates single-molecule long-read sequencing (LRS) and single-cell ATAC-seq (scATAC-seq) data for high-resolution annotation of noncoding variants.
• Structural variation annotation: Contains annotations for over 108,317 structural variations (SVs) and evaluates their potential impacts on 3D chromatin architecture.
• Single-cell resolution: Evaluates accessible chromatin peaks flanking variants across 126 cell types/subtypes in 15 human fetal tissues and 54 cell types/subtypes in 25 adult tissues.
• Expanded Hi-C data integration: Integrates Hi-C chromatin interaction data from 49 human cell types to map long-range chromosomal contacts.
• Chromatin-loop mapping: Links noncoding variants to interacting genes via chromatin loops to associate variants with potential target genes.

Scientific Applications:

• Gene regulation studies: Enables identification of regulatory links between noncoding variants and gene expression via 3D chromatin interactions.
• Disease association research: Facilitates prioritization of noncoding SNPs and SVs that may disrupt genomic architecture and contribute to disease mechanisms.
• Developmental biology: Supports investigation of tissue- and developmental stage-specific regulatory mechanisms using fetal and adult single-cell chromatin data.

Methodology:

Integrates LRS and scATAC-seq with Hi-C chromatin interaction data; evaluates accessible chromatin peaks flanking variants across specified fetal and adult cell types; annotates structural variations (>108,317 SVs) for potential effects on 3D genome organization; links variants to interacting genes via chromatin loops.