rVarBase: an updated database for regulatory features of human variants

Abstract

We present here the rVarBase database (http://rv.psych.ac.cn), an updated version of the rSNPBase database, to provide reliable and detailed regulatory annotations for known and novel human variants. This update expands the database to include additional types of human variants, such as copy number variations (CNVs) and novel variants, and include additional types of regulatory features. Now rVarBase annotates variants in three dimensions: chromatin states of the surrounding regions, overlapped regulatory elements and variants’ potential target genes. Two new types of regulatory elements (lncRNAs and miRNA target sites) have been introduced to provide additional annotation. Detailed information about variants’ overlapping transcription factor binding sites (TFBSs) (often less than 15 bp) within experimentally supported TF-binding regions (∼150 bp) is provided, along with the binding motifs of matched TF families. Additional types of extended variants and variant-associated phenotypes were also added. In addition to the enrichment in data content, an element-centric search module was added, and the web interface was refined. In summary, rVarBase hosts more types of human variants and includes more types of up-to-date regulatory information to facilitate in-depth functional research and to provide practical clues for experimental design.

A childhood acute lymphoblastic leukemia genome-wide association study identifies novel sex-specific risk variants

“…Complementary annotations were performed using CADD, [29] RegulomeDB, [30] HaploReg v4, [31] SNiPA, [32] and rVarBase. [33] GWAS3D was used to predict genetic variants or variants in linkage disequilibrium (LD) affecting regulatory pathways and essential disease/trait associations by integrating functional genomics, chromatin state, sequence motif, and conservation information. [34] It also provides visualization tools to comprehend the results.…”

Identifying Liver Cancer-Related Enhancer SNPs by Integrating GWAS and Histone Modification ChIP-seq Data

“…Thirdly, we mapped the liver cancer-related LD SNPs to the identified enhancers in liver cancer and obtained liver cancer-related enhancer SNPs. Finally, we used a curated regulatory SNP database named rVarBase [ 18 ] to validate our results.…”

“…rVarBase is a database that provides reliable, comprehensive, and user-friendly annotations on variant's regulatory features [ 18 ]. It includes regulatory SNPs (rSNPs), LD-proxies of rSNPs, and genes that are potentially regulated by rSNPs.…”

rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks

“…Considering the distribution ratio of coding and non-coding regions on the human chromosome as well as the increased evidence of the association between non-coding regions and a variety of human traits ( 3 , 4 ), the regulatory annotation of trait-associated SNPs has become more and more important in related studies. Therefore, we developed the rSNPBase ( 5 ) to provide a reliable regulatory annotation of human SNPs; we further expanded the annotation to include several types of known and novel human variants in the updated rVarBase ( 6 ). In the past four years, the two databases have been used in many disease genetic studies ( 7 ) and SNP functional studies ( 8 ).…”