What is new?
rVarBaseis the updated version of rSNPBase. It is consistent with the old version in utilizing experimentally supported regulatory elements from ENCODE and other data resources to make relevant annotation (such as involved regulatory manner and potential target gene). There are several new features in the current version:
New variant types
Compared with the old version, rVarBase provides annotation on more types of human variants, such as known CNV(less than 1M), novel SNV and structure variants.
New dimension of annotation
Besides of experimentally supported regulatory elements and potential target genes, chromatin state of the surrounding region was added to annotate regulatory feature of variants. We utilized 8 active states and 3 bivalent states from the 15-state model that generated by Roadmap final data and ENCODE epigenetic data to provide annotation.
New regulatory manner
Besides of the five regulatory manners (CpG-mediated, TF-mediated, interactive chromatin-mediated, miRNA-mediated, and RBP-mediated) in the old version, lncRNA mediated regulation was introduced to annotate variants; besides of mature miRNA, miRNA target region was involved in variant¡¯s annotation of miRNA-mediated regulation.
More detailed annotation on variant overlapped TFBS
To facilitate in-depth functional research and provide practical clue for experiment-designing, more detailed information of variant overlapped TFBS (often less than 15 bp) in experimentally supported TF binding region(~150 bp) and binding motif of matched TF was provided.
More extended data
More types of extended variants and variant¡¯s associated phenotypes were involved, including: LD-proxies of known SNP, SNP/CNV that is overlapped with or located in queried variant, traits (disease and expression quantitative trait) associated with variant
New search manner
Element centric search module were added and the web interface of the database was refined to facilitate data search and download