---
# System prepended metadata

title: pheWAS

---

## pheWAS

Using this script: https://github.com/mae47/Convergent_evolution/blob/main/BXD_mice/Scripts/overlap_bed_gn.py 

It loops through the BED file data (that contains SV's validated positions) and checks for overlapping positions with the JSON data (HXB traits), considering a margin around the start and end positions. If an overlap is found, it adds the chromosome, position, and trait to a set.

These are my SVs:
| Marker | POS(Mb) | 
| -------- | -------- |
| chr12_1942010    | 1.94201     | 
|chr12_5400029  |  5.400029|
|chr12_10439065 | 10.439065 |
|chr12_32555056 | 32.555056|
|chr12_1719957  | 1.719957 | 
|chr12_21719960 | 21.71996| 


Without margin I didn't find anything:

If I put 5 Mb as margin, I find this trait.
| CHR | POS(Mb) | TRAIT|
| -------- | -------- |----|
| chr12    |       29.402843  (our SV shoud be: chr12_32555056)  | 10060|

If I put 10 Mb as margin:
| CHR | POS(Mb) | TRAIT|
| -------- | -------- |----|
| 12    |       29.402843  (our SV shoud be: chr12_32555056)  | 10060|
|12  |    20.394728 (our SV shoud be: chr12_10439065)  |    10038|

If I put 20 Mb as margin:
| CHR | POS(Mb) | TRAIT|
| -------- | -------- |----|
| 12    |       29.402843  (our SV shoud be: chr12_32555056)  | 10060|
|12  |    20.394728 (our SV shoud be: chr12_10439065)  |    10038|
|12   |   46.50519  |      10175|


### Let's see what happened for the associations found 10 Mb near to our SVs:

#### Search for 10060 trait:

![Screenshot from 2024-03-27 18-38-54](https://hackmd.io/_uploads/HJ_lJ4zyA.png)

![Screenshot from 2024-03-27 18-39-18](https://hackmd.io/_uploads/r1QbkEzy0.png)

![Screenshot from 2024-03-27 18-39-18](https://hackmd.io/_uploads/rkEBy4MJA.png)

#### Compute the mapping for chr12:
![Screenshot from 2024-03-27 18-39-42](https://hackmd.io/_uploads/SksDy4zJA.png)

#### There is also the gene that is present in our SV's region:
![Screenshot from 2024-03-27 18-41-38](https://hackmd.io/_uploads/Sk_4k4MJR.png)

Gene: https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=102552690

Phenotype: https://pubmed.ncbi.nlm.nih.gov/1338076/

Position Our SV: http://useast.ensembl.org/Rattus_norvegicus/Location/View?r=12:32554878-32555357;db=core;time=1697922504734.734

Can we write something like that?

Using GeneNetwork we find that pretty close to our SV (5 Mb), there is an already qtl that mapped to a trait (ADP-induced platelet aggregation) ADP-induced platelet aggregation in platelet-rich plasma in spontaneously hypertensive rats (SHR) was significantly decreased compared with in normotensive Brown Norway (BN) rats. However, in recombinant inbred strains, derived from (SHR × BN) F2 hybrids, correlation analysis revealed that platelet aggregation and blood pressure are independent traits. One of the gene possible related to this trait is the same gene in which our SV is.


Searching for the other trait (10038):

![Screenshot from 2024-03-27 19-11-52](https://hackmd.io/_uploads/B1mSLEMJA.png)

There is again the gene in which our SV falls:
![Screenshot from 2024-03-27 19-11-52](https://hackmd.io/_uploads/HkUHIVM1C.png)
Trait:
