# Optional: Additional options for annotating regions

In addition to annotating regions with overlapping genes, other annotations can be to characterize the regions showing copy number variation.

For example, *Overlap with known SNPs* in the *Copy Number* workflow gives the option of annotation regions with SNPs from dbSNP or a custom SNP database (Figure 1).

![](/files/1CrnABZZIHAtUyfNpWdH)

Figure 1. Annotate regions with SNPs from dbSNP

This task adds two column to the region list spreadsheet - the list of SNPs described in each region and the total number of SNPs in the region. If the list of SNPs is very long, you can output a separate list by right-clicking on the row header and select *Create list of dbSNP* from the pop-up menu.

Another option in the workflow is *Test for known abnormalities.* Selecting this option compares the regions listed in the region list with a database of genomic abnormalities characteristic of particular diseases or syndromes to find possible matches. Annotation options include a Partek-distributed database of 60 syndromes or a custom database (Figure 2). Please note that the included table of known abnormalities is distributed for research use only.

![](/files/YG2OBF22R6stgKLeYRSX)

Figure 2. Test for known abnormalities in your copy number data

If you like to add a custom database, organize the following information by column: the name of the abnormality, chromosome number, start location, and stop location. The input for the task should be a list of aberrations for every sample; do not include unchanged regions in the input or every syndrome will be shown as positive.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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