Commentaries:
Jamieson, Fausset, and Brown
there I will meet with thee, and I will commune with thee from above the mercy seat—The Shekinah, or symbol of the Divine Presence, rested on the mercy seat, and was indicated by a cloud, from the midst of which responses were audibly given when God was consulted on behalf of His people. Hence God is described as "dwelling" or "sitting" between the cherubim.
Other Jamieson, Fausset, and Brown entries containing Exodus 25:22:
Genesis 3:24
Numbers 7:89
Psalms 28:2
Psalms 73:17
Isaiah 37:16
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