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3DSNP

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A database for annotating human noncoding variants by exploring their roles in the distal interactions between genes and regulatory elements. 3DSNP integrates 3D chromatin interactions, local chromatin signatures in different cell types and linkage disequilibrium information from the 1000 Genomes Project. It provides informative visualization tools to display the integrated local and 3D chromatin signatures and the genetic associations among variants. 3DSNP is a valuable resource for the annotation of human noncoding genome sequence and investigating the impact of noncoding variants on clinical phenotypes.

RBP-Var

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Provides annotation of functional variants involved in post-transcriptional interaction and regulation. RBP-Var provides a user-friendly web interface, allowing users to rapidly find whether SNVs of interest can transform the secondary structure of RNA and identify RBPs whose binding may be subsequently disrupted. Moreover, RBP-Var can assess the impact of each SNV on miRNA–RNA interaction as SNVs may destroy or create miRNA-binding sites, which result in loss-of-function and/or gain-of-function miRNA–RNA interactions. RBP-Var is a useful resource for benchmarking the mutations or RNA-editing events that cause disease by changing post-transcriptional interaction and regulation.

SNP2TFBS

An automatically generated comprehensive database of SNPs affecting one or several TFBSs from the JASPAR database. SNP2TFBS consists of a collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor binding sites (TFBSs). A SNP's effect on transcription factor (TF) binding is estimated based on a position weight matrix (PWM) model for the binding specificity of the corresponding factor. These data files are regenerated at regular intervals by an automatic procedure that takes as input a reference genome, a comprehensive SNP catalogue and a collection of PWMs. SNP2TFBS is accessible over a web interface, enabling users to view the information, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.

FIRE / Functional Inference of Regulators of Expression

Scores all single nucleotide variations (SNVs) in the human genome. FIRE is a genome-wide variant annotation tool that predicts the potential of SNVs to regulate gene expression, assigning higher scores to SNVs that are more likely to alter the expression levels of nearby genes. It provides a set of 23 random forests (RFs) trained using a chromosome exclusion approach. In addition, FIRE is specific to expression regulation at the mRNA level.