Store and search on variant and annotation data I need to store a large number of variants with their annotations. I need to import dbSNP, as well as Clinvar, and ExAC etc. Also I have sample variant data from patients. I need to be able to search on genomic regions as well as annotations. And it needs to be scalable.
What would be a preferred data storage technology for such a case? What is the industry using? It needs to be accessible by APIs/REST.
We are using ElasticSearch, but that is proving to be expensive in terms of servers needed.

Something similar to this has been discussed in 
The state, limitations and comparisons of large variant stores, but that post is a little old, I am sure there has been progress since then.
The question you linked is about storing genotypes. Your question is about keeping site information, which is different and much easier.

As to solutions, you can parse the information you want and store them in a standard SQL database. You can use UCSC binning for region queries. Modern SQL databases all provide R-tree indices, which can be adapted for region query and is probably better these days.