"So vs in that" and "So vs As"

[polite]

Hello,

I am confused about " So vs In that" and " So vs As". I don't understand this difference.

I will write some questiones about TOEFL:

1. Among human chromosomes, the Y chromosome is unusual ____ most of the chromosome does not participate in meiotic recombiantion.
a. in
b. so
c. and
d. in that

The response is d. Why? I thought the response was b.

2. ____ sucked groundwater from below, some parts of the city have begun to sink as much as ten inches annually.
a. Pumps have
b. As pumps have
c. So pumps have
d. With pumps

The response is b. Why? I thought the response was c.

I hope your opinions about it. Thanks :)

[Tdol]

1 If you use 'so', then the logic is distorted- implying that the behaviour is a consequence of being unusual- which would imply that any unusual gene would behave in this way. The correct answer shows that the characteristic that makes it unusual is the non=participation.
2 As- means 'because' here- you can't put 'so' in this part of the sentence- it would come before 'some parts'.