En-oma Shrine is beneath a whirlpool in Lake Hylia and can be opened with the crystal on the island above.

Shrine Location
En-oma shrine is located at 0111, -2511, -0088, under the whirlpool in Lake Hylia.
How to Reach En-oma Shrine
Swim to the whirlpool in Lake Hylia, or build a boat with Zonai devices to reach it, or glide down into it. The shrine is near where you land after the whirlpool draws you in.
How to Open En-oma Shrine
Check on the empty shrine to start the quest The Lake Hylia Crystal. If you have enough stamina, you can go to Nachoyah Shrine, use Ascend to reach the top of the island, and use the Paraglider to go south from there to the island above the whirlpool in Lake Hylia. On that island, you can drop the shrine crystal down through the hole in the floor and it will be pulled down into the whirlpool. Let the whirlpool take you down into the cave beneath the water and you can put the crystal in the shrine to open it.
Rauru's Blessing
En-oma Shrine is a Rauru's Blessing shrine. The chest in the shrine contains a Mighty Zonaite Sword.