I suggest to use these installation steps instead:
a) install miniconda
b) install Jupyter Notebook with miniconda

Anaconda does a great job with packaging and integration. If you want to 
use conda anyway, it is best to do as much as possible with it. Unless your 
requirements are very special, there is no point in trying to configure a 
separately installed Jupyter Notebook server to run kernels in a miniconda 
environment. You'd need to write glue code, for example wrapper scripts 
that activate a conda environment when starting a kernel. There are 
Anaconda packages that do this automatically, you just have to use them.

hope that helps,
  Roland

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