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answers:

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URL: http://hartford.uconn.edu/director/academic_plan.html

The URL links to an an HTML page that uses 'object' to display PDF document. Which is blocking the jQuery drop down menu. I have tried using CSS z-index property with positioning specified. Also tried setting wmode="transparent" / wmode="opaque" / and other variations but nothing seems to work.

+1  A: 

If you convert the PDF to an SVG file, then you can embed that directly in your HTML without needing any Javascript. Most modern browsers allow SVG to be embedded.

There are a lot of options for converting PDF to SVG, e.g., pdf2svg, or you can do this with pdftex.

Charles Stewart