Their seat was the castle of Harrenhal, which was granted to them by Aegon the Conqueror as a reward for their service in the War of Conquest. However, the Qoherys eventually became extinct, and the castle was passed on to House Towers.
In the books
The founder of House Qoherys was the castellan of Dragonstone. Their line did not last long: soon after Aegon the Conqueror's death, less than forty years later, the founder's grandson was killed in a rebellion, and all of the castle's inhabitants were put to the sword, rendering House Qoherys extinct. They were replaced as the rulers of Harrenhal by House Harroway.
Houses from the Riverlands