Once you have the key, get inside the apartment and open the large safe to retrieve the rune inside, on the left. In an off-chance you can’t get the code from the Art Dealer; it is 879.
House of Pleasure – Hounds Pit Area
Rune #16, #17 Location. You will find the first in the sewer under the Hounds Pit, near the two Weepers just past the gate. Look for the first underwater and second on top of the cabinet.
Mission 4: The Royal Physician
Rune #18 Location. After you have crossed the tracks, drop down to the road and take the alley. From behind the building that you see, blink up to the balcony above to retrieve this rune from the doorway.
Rune #19 Location. You will find this rune inside Pratchett’s house. To get access to the house, kill Pratchett or steal the key to the house. Once inside the house, look at the paintings on each floor to crack the combination code for the safe. It’s 473, if you can’t figure it out! Grab the rune inside and go your way!
Rune #20 Location. Exit Pratchett’s house through the balcony on the right and blink to the balcony across the way. From there, blink to the next balcony on the right and enter the house. Go around the corner to find the rune in Outsider Shrine.
Rune #21 Location. After entering Midrow Substation and disabling lights, look for this rune on a desk in front.
Rune #22 Location. After reaching Sokolav in his greenhouse, look for this rune on the desk, on the left side of the room.
Mission 5: Lady Boyle’s Last Party
Rune #23 Location. At the start of the mission, take the street and go to the security checkpoint on the left. Go right to enter the doorway in the red wall and follow the stairs up, and you should come to an open blue door. Go through it to find an Outsider Shrine with a rune on it.
Rune #24 Location. Jump into the water at the far end of the river that runs through the center of the city. You should find the rune under the water, somewhere in the center.
Rune #25 Location. Take the stairs on the left of the courtyard entrance inside the mansion and go through the kitchen leading to the barred door. Use the switch on the right to open the door and go to the far-right corner. You need a key to open the vault here. Get it from the desk in Lydia’s room on the second floor.
Mission 6: Return to the Tower
Rune #26 Location. When you are outside the tower having climbed the water lock, go right towards patrolling tallboys and enter the small building. You will find the rune on the shelf inside that building.
Rune #27 Location. Go to Lord Regent’s personal chambers on the second floor and look for the chest. You will find this rune inside that chest. You will need a key to open that chest and that, you will find on a dresser in one of the bedrooms down the hall. After retrieving the key, take the double doors at the end of the corridor to come back to Lord Regent’s room.
Rune #28 Location. When you are in the tower, take the stairs in the corner to the right by the large stairs in the main foyer. You will reach Torturer’s room in the basement using these stairs, and once you are inside, look for an outsider shrine in the corner with this rune.
Rune #29 Location. After reaching the tower rooftop, look for this rune in the planting room. You will have to disable the light wall by taking the stairs on the left past the library and enter the planting room.
Return to the Tower – Hounds Pit
Rune #30 Location. Duel Lord Shaw and speak to Pendleton about Boyle mission to get this rune.
Rune #31 Location. You will find this rune in the Hounds Pit. Do not slaughter Boyle sisters and they will give you this rune. You will find it in their room. You will get the clue about the rune at the tavern’s entrance near the Wallace and second note by the rune will reveal the identity of your benefactor.
Rune #32 Location. Speak to Callista in the bar and try to locate Emily. You can use your Dark Vision to find Emily. She will most probably be in Corvo’s room, in the corridor furthest from the bed. Emily will give you the rune.
Mission 7: The Flooded District
Rune #33 Location. When you are getting your gear in the refinery, you will lower a drawbridge to climb down the chains. When you are climbing down your first chain, use a valve wheel to open a large door to get outside and retrieve this rune from the ground across you.
Rune #34 Location. After retrieving Daud’s Key, come back to the entrance to the assassin hideout and use the door next to it. Go through the door and climb down the chain and look for this rune on the bottom.
Rune #35 Location. From the last building to the left before the train tracks, jump out of the window to the adjacent building on the left. Go to the roof to find this rune out in the open.
Rune #36 Location. When you encounter Granny Rags in the sewers, help her to get this rune as a reward. You can retrieve it from an Outsider Shrine in her room at the second floor of her apartment.
Rune #37 Location. After you have retrieved the sewer master key, return to the entrance of the sewer and open the gate. You will find this rune on the lower level.
Mission 8: The Loyalists
Rune #38 Location. After returning back to the Hounds Pit Tavern, go to Piero’s shop and look for this rune on the second floor.
Mission 9: The Light at the End
Rune #39 Location. After reaching the fort, take the sewers on the right leading to a valve that opens another sewer door. Go through that door and opening on the left that leads to the Gatehouse Drainage and look for this rune on the ground.