With this addon - https://marketplace.atlassian.com/apps/1218767/smart-ql?hosting=server&tab=overview - you can query JIRA with SQL straight from the app or through the special JDBC without to worry about permissions to data.
All custom fields are stored in customfields table in Jira.
Also you can find options and values in customfieldoption and customfieldvalue tables.
Is that what you were asking for?
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Something simple to get you started? :
select * from customfield limit 10;
select * from customfieldoption limit 10;
select * from customfieldvalue limit 10;
How are you intending to query?
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