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If e.g. a project variable (with the '@variable') notation is used in the filter field of a value relation widget, this doesn't work. While configuring it does work, but when closing the layer properties and actually using the widget, it doesn't.

I have looked into the source code, and I think the problem is (for MASTER) in src/core/fieldformatter/qgsvaluerelationfieldformatter.cpp: no expression context is set. I think in the following block:

if ( !config.value( QStringLiteral( "FilterExpression" ) ).toString().isEmpty() )
{
    request.setFilterExpression( config.value( QStringLiteral( "FilterExpression" ) ).toString() );
  }

...it needs to be changed to something like this:

if ( !config.value( QStringLiteral( "FilterExpression" ) ).toString().isEmpty() )
{
    QgsExpressionContext context( QgsExpressionContextUtils::globalProjectLayerScopes( layer ) );
    request.setExpressionContext( context );
    request.setFilterExpression( config.value( QStringLiteral( "FilterExpression" ) ).toString() );
  }

(Btw. The problem is also present in QGIS 2.18.)