FUMA Output

[sfa...@aucklanduni.ac.nz]

Hi, 

I've run my SNP set (~200SNPs) through the SNP2Gene function (Job number 75923) and the results only came back with 1 SNP in the summary - is this correct or has an error occurred? It seems odd.

Thanks, Sophie 

[DP Wightman]

Hi Sophie, 

It looks like there is only one variant after matching with the 1KG reference. Do you mind posting the first few lines of your input file? I can have a look why the rest of the SNPs aren't matching.

Cheers,

Doug

[sfa...@aucklanduni.ac.nz]

Hi Doug,

Thanks for getting back to me. See below the first few lines:

CHR BP         SNP                 OR                 P

7 23084258 rs10256359 1.1273957 2.00E-12

5 102983270 rs10463554 1.0649627 2.00E-07

3 183042285 rs10513789 1.25 3.00E-10

15 61708933 rs10519131 1.22 1.00E-06

9 74302924 rs10746953 2.62 1.00E-06

11 32874118 rs10767971 3.24 5.00E-07

1 54106570 rs10788972 1.56 6.00E-08

1 232528865 rs10797576 1.131 5.00E-10

1 232528865 rs10797576 1.12 8.00E-13

12 39959194 rs10877840 1.15 1.00E-06

10 15527599 rs10906923 1.0752687 1.00E-08

2 236024319 rs10929159 1.0626993 7.00E-08

17 45436075 rs11012 1.43 6.00E-08

12 122819039 rs11060180 1.1074197 3.00E-10

12 122819039 rs11060180 1.105 6.00E-12

12 122819039 rs11060180 1.1111112 2.00E-20

Thanks,

Sophie 

[Kyoko Watanabe]

Hi Sophie,

It looks like you have SNPs on hg38?

FUMA currently only support hg19, could you please convert to hg19 position then try again?

Also, I see you have multiple SNPs on the same location. Unless they have different alleles, it will cause an error in the FUMA as well.

Best,

Kyoko