Shanks is the son of a Celestial Dragon and Rocks D. Xebec.
I don't think it's a coincidence that Rocks attacked the Celestial Dragons at God Valley. This was probably a union that they could not tolerate (Rocks a D. and a Celestial Dragon, on some Capulet and Montague shit).
Roger when holding Momo remarked to Rayleigh that it reminded him of the old days. He was probably referring to picking Shanks up at God Valley. Garp probably used that same 'sins of the father shouldn't follow the kid speech' on him to convince him to take Shanks (Which is why when he repeated in in regards to Ace it was so effective). Because on the one hand they couldn't kill the son of a Celestial Dragon. On the other they could not have the son of the guy who wanted to take over the world as part of the WG hierarchy. So best for Roger to take him.
When WB meets Shanks he remarks that the scar from that guy ached when he saw him. He could be referring to Roger but seeing as he mentioned Garp, Sengoku and Mihawk in the conversation it makes no sense that he wouldn't refer to Roger giving him the scar. Hell he even mentions Roger when he asked about Buggy. He was referring to Rocks giving him the scar for betraying him at God Valley. Not only that but we know the Rocks members do not like to talk about the old crew, so it makes sense that WB didn't even want to mention his name.
When Rayleigh found out that Shanks didn't tell Luffy that he was on the PK's ship, Rayleigh said that he couldn't in good conscience talk to Luffy about things Shanks didn't tell him. He is probably referring to the circumstances that led to Shanks joining the crew and his past. Shanks probably feels shame about his heritage. The WG also wouldn't reveal that one of the Yonko is the son of a guy they tried to erase from history and a Celestial Dragon. That's why his wanted poster doesn't have his name. You couldn't use the Rocks or the Celestial Dragon surname.
Onto the shame thing, Ace was whining about having the blood of a demon. However how would Shanks feel? On the one hand his father was the embodiment of chaos. Their crew was so chaotic that friend and foe alike were killed by crew members. On the other his mother was a symbol of ultimate control. The Celestial Dragons take control so far that they control living things (slaves). This is also why he cried after Roger came back from raftel. Because he found out just how bad the CD's were and probably found out something unpleasant about the Ds.
This is why Shanks dislikes unnecessary fighting and wants to keep the balance of the world. Because ultimately he is a child split in the middle between chaos and order.