Normaly not, but some MB-manuals tell you, you should use slot 1 for the primary graphiccard - if in doubt, just try it.
On my both ASRock-boards the graphiccard is also working at slot 2 - but slower because they are only PCIe 2.0 x4
And by the way: The fan of the graca is not blowing, it is sucking in, so it will not blow hot air to the LSI-controller ๐
FYI: PCIe slot 1 is connected to the CPU, slot 2 is (sometimes) connected to the chipset. On mainboards which can handle two gracas (with 3 PCIe-slots), slot 1 and 2 are connected to the CPU and provide 2x PCIe x8 (electrical x16/x8). Read your manual for further infos.