It would be the ends of the heatpipes at the top of the heatsink.
I found a decent resolution image of your motherboard, the Gigabyte GA-Z97N WIFI (see the thumbnail below). All mini-ITX motherboards are 170 mm square so by counting pixels I get that the distance from the center of the CPU socket to the center of the PCI-E slot is 96 mm. According to the dimensions of the Dark Rock TF heatsink (second thumbnail below), the distance from the center of the CPU contact surface to the ends of the of the heatsink is 89 mm. Remember, that's to the center of the PCI-E slot. The thickness of the PCB, the graphics card components, and a backplate will decrease the gap between the graphics card and the ends of the heatpipes.
Also, note that rotating the heatsink to this "heatpipes down" orientation will result in the heatsink being 3.5 mm closer to the top of the case (73.58 mm vs. 70 mm).
(As a sanity check I measured the distance from the center of the CPU socket to the center of the first RAM slot and found it to be 53.75 mm. This is just a bit greater than the distance from the center of the heatsink to the outside of the lower curve of the heatpipes which is 52.05 mm, according to be quiet. The RAM module's thickness is why the heatsinnk contacts the RAM module.)
This is incredibly helpful. Thanks so much!