how to separate ground potential

The output impedance and hence short circuit current of the HV supply is also on issue. A 4 kV 1 mA should not be that dangerous :-), unless of course if there is a large (stray) capacitance at the power supply output, which could store a significant charge, which could cause a nasty electric shock flowing through your body. For instance the CRT

There are miniature neon signs within windows advertising a product, in which the leads or connections could be touched. The short circuit current is so small that it does not do any harm.

Other typical examples would be simple ionizer with about two dozen rectifiers and capacitors in a voltage multiplier chain, fed directly from the 230 V mains. You could touch the output of the chain, but of course it is a good idea to have a 1 megaohm at the output to limit the current in case of the extremely rare situation that _all_ rectifiers and capacitors would fail and you would have 230 V mains at the other end of the resistor.

We do not know if the original poster is using such high impedance HV source, but in that case using a high isolation transformer to feed the 5 V side, the transformer stray capacitance (perhaps less than 10 pF) may feed 50/60 Hz hum into the HV line.

Paul