Question: I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of phenotypic effects with some additional metadata. Thank you in advance.

Answer: 
You can search by traits (mostly diseases) for genome wide association, in these databases:

* [Gwasdb2](http://jjwanglab.org/gwasdb)
* [Human genome variation Database](https://gwas.biosciencedbc.jp/): it also links to a Copy number Variation (CNV) database.
Just to make this post a tiny bit more useful, I must add that there are several additional sources I've found:

* UniProt has an open dataset called `humsavar`
* ClinVar database
* HGMD database
* OMIM
* A [paper](http://www.ncbi.nlm.nih.gov/pubmed/25552646) with a manually collected database based on recent publications in Nature Genetics.

Different datasets intersect to some extent, but all in all you get over 200k somewhat validated SNPs.