In the comics, you have Project Rebirth, which seems to be just an Army experiment, and then later on you have SHIELD. But the MCU said, "well, in real life the CIA was preceded during war time by the OSS? What if SHIELD was the same way?" Enter the SSR. This also allowed them to give the Howling Commandos ties to SHIELD despite not being led by Nick Fury in this continuity.
Which brings us to another alternate reality, but one in the comics this time: Spider-Gwen. Spider-Gwen is set on Earth-65, which is similar to the main Marvel universe on the surface, but with differences here and there. The differences generally fall into one of two categories - (1) characters are the opposite of what you'd expect; Peter Parker was the Lizard, Matt Murdock is the Kingpin, Frank Castle is a cop, or (2) women are put to the forefront; Gwen Stacy is Spider-Woman, Peggy Carter runs SHIELD, Captain America is named Samantha Wilson.
In Spider-Gwen #2 (November 2015), we get a lot of Captain America's backstory. The first part comes in a flashback, where we see the SSR in action:
It's not the 616 universe, which is a little disappointing, but I'm hoping this is the first step to learning the organization existed there in some capacity as well.