UTG (Hero): $ 1400
MP : $ 200
CO : $ 1380
BU : $ 200
SB : $ 200
BB: $ 200

Pre Flop: (pot: $6.00) Hero has Q J T 9 6
Hero raises to $14, MP folds, CO raises to $48, BTN SB BB folds, Hero calls

Flop: ($102, 2 players) J T 2
Hero checks, CO bets $102.

Turn: ($306, 2 players) 4
Hero checks, CO bets $306, Hero is allin at $1,250

Villain is solid reg, dont have specific reads on him.

After going all in and did some equity calculations, I realised I am actually a underdog against most of the hand that would call there.

Against
Sets 16%
AAKQX with FD and AA with double FD 45%
AAXXX, AKQT9 with FD and AA with FD 55%

The best i can hope for is he overplaying his bare aces which is a very low possibility.

How should i approach this?

There are lots lots more combos of good draws in his range than sets, partly due to combinatorics (you block them) and partly because people don't 3bet that much with JJ or TT in their hands. You're most likely up against a big draw and have 45-55%.

If you think he plays rivers well, i.e. value-betting thin, good balanced sizing, some bluffs, then you should get it in; if you think he plays rivers badly, you can consider calling. I highly doubt he has much of a pot-pot-pot-fold range so don't expect to have any fold equity.