SNP missing in the snps.txt of results

[Qianhui Xu]

Dear FUMA team,

I am seeking your assistance regarding certain SNPs missing from the snp2gene results. I submitted job ID 646233 to annotate significant SNPs, but rs34333163 does not appear in the output. I have verified that this SNP exists in the 1000 Genomes European panel and is located outside the MHC region. Additionally, I did not provide effect or non-effect alleles in the submission. Could you please help me understand why this SNP might be missing?

Thank you for your support.

Best regards,

Xu

[Tanya Phung]

Hi, 

Please send the files p4_tinnitus.txt and p4_tinnitus_lead.txt to the fuma email address so I can take a look further. 

Best,
Tanya

[Qianhui Xu]

Dear Tanya,

I have sent the files to the fuma email address, thank you for your help.

Best,

Xu

[Tanya Phung]

Hi Xu, 

The SNP  rs34333163 does not exist in your p4_tinnitus_lead.txt file:
grep rs34333163 p4_tinnitus_lead.txt returns nothing

grep rs34333163 p4_tinnitus.txt
rs34333163      4       103283117       8.52E-05

8.52e-5 is greater than the genome-wide threshold 5e-8 so this snp was removed. 

Best,
Tanya

[Qianhui Xu]

Hi Tanya,

Thank you for checking this. rs34333163 is not a predefined lead SNP, which is why it does not appear in the p4_tinnitus_lead.txt file. In p4_tinnitus.txt, indeed all SNPs have p-values greater than 5e-8, but the significant SNPs I used were obtained through other approaches, independent of the GWAS p-values. However, rs34333163 is the only SNP that is missing from the results table, so I am not sure this alone explains its absence. Could there be any other possible reason why this SNP does not show up?

Best regards,
Xu

[Tanya Phung]

Hi Xu, 

You submitted the file p4_tinnitus.txt to SNP2GENE, there are 8 variants in this file, and all of them have p value e-5 which is less than the significant threshold e-8. By definition, these 8 variants did not reach significant threshold and would be removed. 

However, you also included a lead snp file, which contains 4 variants. When a list of lead snps is included, the p value is not taken into consideration. These 4 SNPs are then present in your output: 

This is the list of lead SNPs you submitted

These 4 snps are in the result table for your job 646233

As explained in the previous message, the SNP that you're asking about rs34333163 has p value < 5e-8 so it is removed.

Best,
Tanya