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A list of SNPs using dbSNP IDs can be imported as a text file and associated with an annotation file as described for a list of genes. The annotation file (genomic database) you use to annotate the SNPs should minimally contain the genomic coordinates (chromosome number and physical position) of the locus. Please be aware that using hg19_dbSNP_v2.pannot as the annotation source is very memory intensive due to the file’s large size. Including the genomic coordinates of the SNPs if you have them (see Starting with a list of Genomic Regions) saves having to look-up genomic coordinates from the dbSNP name. 

Novel SNPs, or SNPs that are not found in your annotation source, must be imported as a region list. The only difference would be to use the SNP name in place of a region name.

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Starting with a list of SNPs that have been associated with genomic coordinatesloci using an annotation file and assigned a species with genome build, you may use Find Overlapping Genes to annotate these SNPs with the closest genes. 

• Select Tools from the main toolbar
• Select Find Overlapping Genes
• Select Add a New Column with the Gene Nearest to the Region from the method dialog

If you have not specified the species or added an annotation file, the Edit Genome dialog will open

• Select the species 
• Select OK
  

The Report Regions from the specified database dialog will open.

• Select your preferred database

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• Select OK

This will add 9 3 columns to the list of SNPs spreadsheet including Nearest Feature, which will indicate the nearest gene and strand. To allow gene list operations such as GO Enrichment or Pathway Enrichment to be performed on the SNP list, we can set the Nearest Feature column as the Gene Symbol column.  

• Right click the spreadsheet in the spreadsheet tree
• Select Properties from the pop-up menu
• Select Gene symbol instead of Marker ID 
• Select Feature in column and select Nearest Feature
• Select OK

Annotating a Partek Genomics Suite-generated SNP list with SNVs

If you have a SNP spreadsheet that was generated using Partek Genomics Suite, you can annotate the SNP list with gene, transcript, exon, and information about the predicted effect of the SNPs. 

• Select Tools from the main command toolbar
• Select Annotate SNVs

Starting with a Region List

A region list in PGS must contain the chromosome, start location, and stop locations as the first three columns, respectively. The chromosome name (or number) in the region list must be compatible with the genomic annotation for the species if you plan to use any feature (like motif detection) that requires reference sequence information. 

• Import the region list as described above. Select Other for data type. Chromosome name or number should be imported as a text field; location start and stop may be either integer or text.