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ClinTAD is a tool to quickly evaluate the clinical relevance of copy number variants (CNVs) in the context of topologically associated domains (TADs). Instructions for using the tool are below.

Single
If you have data for a single patient, the Single tab can be used to visualize the relationship between a copy number variant and nearby TADs.

Chromsome: Enter the chromosome number as an integer (e.g. 1 or 2), X, or Y
Start: Enter the coordinate of the start of the CNV
End: Enter the coordinate of the end of the CNV
Phenotype: Optional. Enter any relevant phenotypes for your patient using HPO IDs. Phenotypes can be entered as integers or as full HPO ID numbers. For example, if a relevant phenotype is "cleft upper lip", enter HP:0000204 or just 204.

The HPO Phenotype Lookup form can be used to look up the HPO ID number for relevant phenotypes. For example if your patient has a cleft lip, enter "cleft" and press the lookup button. A list of HPO IDs with the word "cleft" in the name, def, or comment field will then be added to the dropdown menu. Press the add button once a phenotype is selected to move the ID to the Phenotypes form.



Multiple
If you have data for multiple patients, the Multiple tab can be used to determine if there are genes with the specified phenotypes near a CNV. Phenotypes must be seperated by commas, and each patient/case should be on it's own line. Input is in the following format:

Patient Identifier (tab) Chromosome Number (tab) CNV Start (tab) CNV End (tab) Phenotypes (new line)
Patient Identifier (tab) Chromosome Number (tab) CNV Start (tab) CNV End (tab) Phenotypes