Why does it sound sharp???

[johnsid]

I recently replaced strings on my Mexican Jazz Bass with heavier gauge (50-110) and I believe I have followed every step here ,the only difference is that string height is set a little bit lower, but when I press the 4th string on the 1st fret(tuned D#/G#/C#/F#) E sounds annoyingly sharp.
What could be wrong?

[Febs]

Make sure that the string is properly seated in the nut slot. If the nut is too high or the string is not properly seated in the slot, you will pull the string sharp as you depress it on the lower frets, particularly the first fret. If it is seated properly, you might need to have the nut slot filed.

[96tbird]

If you haven't yet, "Witness" the strings. This means place your thumb right where the string exits the nut to the fretboard, and bend it down so it doesn't arc up over the nut, so that it is a perfectly straight run from nut to saddle. Do the same to all strings where they come over the saddles. Retune and intonate. See if that helps.

It sounds like you are new at this and this important detail is not mentioned in any guide I have seen so is overlooked by new folks. If it doesn't help, as FEBS said, the nut may need work.

A quick trick to estimate the nut condition:
#1 fret the third fret, press down on the string directly above the first fret and take note of how much travel is between the string and 1st fret top.
#2 Now fret the first fret, and see how much travel between the string and the second fret top.
The two distances of travel should be the same. If travel of #1 is more than travel of #2, your nut slot needs to be filed down a bit.

[johnsid]

That's what I 've been missing (some extra filing), thank you for the advice.