SNP annotations

[zx8754]

Annotate input association and LD file with following datasets:

• clinVar - UCSC table
• GWAS catalog
• HaploReg v4
• gTEX
• VEP
• CADD
• ACMG

[JulieGb]

Hi everyone,

I'm using the online version of locusexplorer.
When I submit my own association & LD files, the manhattan is plotted and I also have the LD and the imputed/typed SNP. But I don't have the annotation of the SNPs.

Here is the header of my association file :

"CHR BP SNP P TYPED
chr2 218098969 rs2373042 0.77552258 1
chr2 218099122 rs112887086 0.508767204 1
chr2 218099143 rs2373043 0.642652653 1
chr2 218099677 rs2565696 0.733405434 1"

Do you have an idea of my issue?

Thanks

Julie

[zx8754]

Hi @JulieGb

This feature is planned for version 0.8. At the moment, version 0.7, has annotations only for Prostate data, see this folder for annotation files used for Prostate data:
https://github.com/oncogenetics/LocusExplorer/tree/master/Data/Annotation

We are also planning to add functionality to upload custom annotation files:

• Issue Multiple Bed files as input #6

• Issue Multiple region as one upload #10

[JulieGb]

Hi @zx8754

Thank you for your answer.
Why does it work only for Prostate data ? The annotation step doesn't require the SNP ID of my association file with the aim to match with your association file ?

Because I'm actually working on genetics data from the Oncoarry consortium (like Practical), so I potentially have the same SNP ID as Prostate data.

[zx8754]

It could be that, annotation file SNP rsids do not match with your SNP rsids. Annotation is limited to Prostate finemapping regions only.

I have just tested with one of the finemapping regions - chr10_103914221_104915094. I downloaded this region association and LD files from GitHub. Then uploaded as custom data using LocusExplorer website, and annotation tracks shows up. See below:

Also, please feel free to email me your files, so I can test further locally.