To get technical, the red lights you see ontop of skyscrapers and other tall structures are officially termed "obstruction lights" by the FAA. Their application, and the height of the structures they are required upon, is all dependent on the flight path and/or glide slope to airports. For example, next to New York LaGuardia Airport, there is a two-story apartment building with red obstruction lights ontop. This building also happens to be near the threshold of Runway 4, very close to the touchdown zone on the pavement of the runway.
Flashing red, solid red, flashing strobe light white, they are all dictated by the FAA, resulting from an equation taking into consideration: height of the structure, and said structure's location within a designated flight path or glide slope approach.
Hope this helps!
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