Genetics: Chromosome 17 CA10

[Jonathan Edwards]

So it seems there is a shared variant associated with ME/CFS, multisite chronic pain, and ease of getting up in the morning.

Fascinating. Keep at it.

 

[forestglip]

That's an amazing match with the 'Ease of getting up in the morning' gene. Very impressive investigation FG.


I'm not understanding why the x axis in the neck shoulder pain chart is different. Can you help me understand?

It's using an older assembly/coordinate system called GRCh37. The more recent one that DecodeME uses is called GRCh38. Defining where exactly a SNP is on a chromosome isn't an exact science, so as they learn more, they make updates to the positions.

"Liftover" is converting the coordinates to a different assembly. I used liftover for the "Getting up in the morning" GWAS to make it match DecodeME.

Spoiler: Quickly converting a SNP

On gnomAD, if you look up a SNP, it'll tell you where that SNP is in the other assembly. For example, here's the page for the lead SNP of the neck and shoulder pain GWAS in GRCh37 coordinates, as reported in Table 2: https://gnomad.broadinstitute.org/variant/17-50259142-A-C?dataset=gnomad_r2_1

Partway down the page, it says:

Liftover
This variant lifts over to the following GRCh38 variant:

• 17-52181782-A-C
  View variant in gnomAD v4.1.1

 

[Hutan]

Thank you, very helpful