...

• Select Tools from the main toolbar
• Select Annotation Manager... (Figure 1)
  

...

• Select Browse... under Source to specify the BED file; a default new file name and destination will populate Result, but this can be changed 
• You can specify the name and save location of the new annotation file under Result; we typically choose the Microarray Libraries folder  
• Specify the Name of the annotation database file
• Select the correct Species and Genome Build for the annotation file from the drop-down menus (Figure 3) 
  

...

The Annotation Manager will display the new annotation in the My Annotations tab (Figure 4)

Visualizing a BED file as an annotation track in the genome browser

...

• Select Next >
  
• Choose the annotation file you created; here we have selected UCSC CpG Islands (Figure 7)
• If your annotation file does not contain strand information for each region, deselect Separate Strands; here we have deselected it

...

...