Regvar tutorials

Brief introduction

RegVar is a deep neural network-based computational server for prioritizing tissue-specific noncoding regulatory variants. RegVar integrates the sequential, epigenetic and evolutionary profiles of SNPs and their potential target genes in 17 human tissues, and give tissue-specific predictions of regulatory probabilities of the provided SNPs on provided genes.

Input

Upload a file containing a list of SNP IDs and genes

A text file containing a list of SNP IDs (indels are currently not supported) and their possible genes is needed to be uploaded to the server for batch analysis. The result will be generated based on all pairwise combinations of the SNPs and genes no more than 10,000 valid pairs.
Click here to see an example file

Or type SNP ID(s) and gene(s) in the corresponding search boxes

SNP ID(s) and their possible target gene(s) are accepted as input in the SNPs and Gene search box, respectively. Multiple SNP IDs or genes should be delimited by commas, spaces or tabs, and if so, the result will be generated based on the all pairwise combinations of the SNPs and genes.

Output

All results will be listed in the Result page, including the basic information of your query data (the positions of the input SNPs and genes, the genomic distance between them) (in GRCh37/hg19 genome coordinates), and the output RegVar scores, which come straight from the tissue-specific RegVar model and are interpretable as the extent to which the SNP is likely to have an effect on the regulation of the corresponding gene in your selected tissue.

A result file containing the same information will be sent to your email address, if you have it input.

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