We have developed a non-coding variation impact prediction tool in the "Regulatory Variant Prioritization" page. Users can use the variation IDs or upload a VCF file to query the predicted variation impacts in our database.
We fixed "Haplotype Network Analysis" page, which is now available.
Chromatin Accessibility Map and Non-coding Varation Scores Map can be seached in "Search for Variation by Gene" page.
We generated high-quality CA data from six representative rice tissues and used these data to train CNNs (AUROC: 0.93-0.95) to predict the impacts of variants on CA in non-coding regions.
We defined a 'Chromatin Accessibility Score' for each variation to evaluate the impact of variations (especially for non-coding variations) based on chromatin accessibility data. This information can be found at 'Search for Variation by Gene' page and 'Search for Variation information by Variation ID' page.
Gene expression atlas added into RiceVarMap, gene expression across the tissues and stages can be queried at "Search for Variation by Gene" page.
We added callus, root, young leaf, flag leaf, and spikelet's chromatin accessibility data to RiceVarMap, which can be searched in "Search for Variation by Gene" page.
Gene symbol and gene name like 'hwh1' can be searched in 'Search for Variation by Gene' page.
new genomic variations and GWAS results, improved annotations of missense variations, integrated chromatin accessibility data for non-coding variations.