This application can be used to determine if genes and variants of interest are located in accessible or inaccessible regions according to the 1000 Genomes and the TopMed accessibility masks. Additionally, the app displays variant density on genotype chips, as well as their accessibility status. Variant position and information for the different chip was downloaded from here ( https://www.well.ox.ac.uk/~wrayner/strand/sourceStrand/index.html ). A manuscript in which we analyze properties of the accessible regions in detail is currently under submission at Human Molecular Genetics.
Fraction of the entire gene body and only the exonic region that is labeled as inaccessible according to the different masks. For GRCh37, data is displayed only for the 1000 Genomes masks.
Try to change genome build or gene HGNC.
For the queried gene, variants which are located on chips are displayed with their chromosomal position on the x-axis. The y-axis displays the number of chips on which the variant is located. The dark filled regions below the plot indicate the regions that are accessible according to the different masks.
Number of variants in the queried gene which are included on the respective genotype chip.
Click on one or multiple rows to display details of these variants on the right table.Details of variants in the queried gene that are included on genotype chips.
Displays accessibility and genotype chip information for the queried variant.