Query on 250 million records
Likely, the issue is caused by the very long IN lists. Instead of using the IN list, create a temporary table with the values you want to filter on. Then rewrite the query as a join:

CREATE TABLE #FilterOutputArea (...) 
INSERT #FilterOutputArea VALUES ('E00139237')
... etc...

CREATE TABLE #FilterColumnID ()
INSERT #ColumnID VALUES (298)
... etc...

SELECT 
[Extent1].[Id] AS [Id], 
[Extent1].[OutputArea] AS [OutputArea], 
[Extent1].[ColumnId] AS [ColumnId], 
[Extent1].[Value] AS [Value]
FROM [dbo].[ColumnValues] AS [Extent1]
JOIN #FilterOutputArea ON ...
JOIN #ColumnID ON ...