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 https://github.com/oncogenetics/LocusExplorer/issues/6

• Issue https://github.com/oncogenetics/LocusExplorer/issues/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.