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I understand that Data Relationships connect two DE in Email Studio and can then be used to filter even more on that. And that Contact Builder attributes are used for Journey Builder.

But can I set up both a data relationship in email studio and a Contact Builder attribute for the same Data Extensions? Could this cause any issues?

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There is nothing wrong with using same Data Extension in both Attribute Groups in Data Designer and Data Relationships in Email Studio. These work fully independently. It is also fairly normal for same Data Extension to be part of multiple Attribute Groups

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