John 1:1-3: "1 In the beginning was the Word, and the Word was with God, and the Word was God. 2 He was in the beginning with God. 3 All things were made through him, and without him was not any thing made that was made."
John 1:10: "He was in the world, and the world was made through him, yet the world did not know him."
John 1:14: "And the Word became flesh and dwelt among us, and we have seen his glory, glory as of the only Son from the Father, full of grace and truth."
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John 1:14 appears in the first verse, specifically in the last line: "Word made flesh, we long to hear You."
The other two verses from John 1 appear in the hymn's second verse, specifically in the line "Word that brought to life creation."
These verses from John are also referenced more generally in the hymn; throughout, there are multiple addresses to the "Word."
The last two lines of the hymn are "Word of truth, to all truth lead us; / Word of life, with one bread feed us." These seem to refer to John 14:6: "Jesus said to him [Thomas], 'I am the way, and the truth, and the life. No one comes to the Father except through me.'"