Genome-wide functional annotation of human multi-nucleotide variants

Genome-wide functional annotation of human multi-nucleotide variants Dataset DOI: 10.5281/zenodo.21549742 Dataset description This dataset contains genome-wide functional annotations of human multi-nucleotide variants (MNVs) and their potential regulatory impacts. Multi-nucleotide variants (MNVs), defined as two or more adjacent nucleotide substitutions occurring on the same haplotype, represent an important class of genetic variation that may exert functional effects distinct from single nucleotide variants (SNVs). In this study, we systematically characterized the functional consequences of human MNVs by integrating multiple regulatory annotations, including transcription factor binding sites, microRNA binding sites, and RNA secondary structure alterations. The datasets provided here include predicted impacts of MNVs on transcriptional regulation, post-transcriptional regulation, and non-coding RNA structures. File descriptions 1. hg38mnv_addgene_oneline Genome-wide human MNV catalog based on the hg38 reference genome Description: This file contains information and annotations for human multi-nucleotide variants (MNVs) identified based on the human hg38 reference genome. Each MNV is represented as a single record, including genomic location, allele information, variant identifiers, and annotation information. This file provides the foundational MNV catalog used for downstream functional annotation and impact analysis. File format: The output file is a tab-delimited text file. Columns: Column Description Chromosome name Chromosome location of the MNV Position Genomic position of the MNV based on the hg38 reference genome MNVID Unique identifier assigned to each MNV Ref Reference allele sequence Alt Alternative allele sequence rsID Corresponding dbSNP reference SNP identifier, if available INFO Variant annotation information and additional metadata 2. tfbs_mrna.txt MNV effects on transcription factor binding sites in mRNA-associated regulatory regions Description: This file contains human MNVs overlapping transcription factor binding sites (TFBSs) within mRNA-associated regulatory regions. The annotations describe potential changes in transcription factor binding caused by MNVs and provide evidence for altered transcriptional regulation. 3. tfbs_lnc.txt MNV effects on transcription factor binding sites associated with long non-coding RNA regions Description: This file contains MNVs located within TFBS regions associated with long non-coding RNA (lncRNA) loci. These variants may influence lncRNA transcription by altering transcription factor recognition motifs. 4. mirbs_mrna.txt MNV effects on microRNA binding sites in mRNA transcripts Description: This file contains MNVs located within microRNA binding sites (miRBSs) of mRNA transcripts. The annotations describe potential alterations in miRNA–mRNA interactions caused by MNVs. 5. mirbs_lncrna.txt MNV effects on microRNA binding sites in long non-coding RNAs Description: This file contains MNVs overlapping microRNA binding sites within long non-coding RNA transcripts. These annotations provide information about potential changes in miRNA-mediated regulation of lncRNAs caused by MNVs. 6. lncRNA_struc.txt MNV-induced structural changes in long non-coding RNAs Description: This file contains predicted structural effects of MNVs on lncRNA secondary structures. The annotations describe structural differences between reference and alternative RNA sequences caused by MNV substitutions. 7. premirna_struc.txt MNV-induced structural changes in precursor microRNAs Description: This file contains predicted structural effects of MNVs on precursor microRNA (pre-miRNA) secondary structures. These structural alterations may influence miRNA processing and maturation. Data format All files are provided as tab-delimited text files. Each file contains: genomic coordinates of MNVs reference and alternative alleles genomic annotations regulatory element information predicted functional impact measurements Detailed descriptions of individual columns are provided in the header lines of each file. Related manuscript This dataset supports the study: "Genome-wide annotation of human multi-nucleotide variants reveals widespread functional differences from single nucleotide variants" Data usage These data can be used for: functional prioritization of human MNVs comparative analysis between MNVs and SNVs investigation of regulatory variation studies of non-coding RNA regulation Citation If you use these data, please cite the associated manuscript: [Manuscript citation information will be added after publication] Access information Other publicly accessible locations of the data: https://gonglab.hzau.edu.cn/HMdb/