Question: difference between 2 snp's data annotations
0
gravatar for mms140130
9 months ago by
mms14013050
mms14013050 wrote:

Hi,

I have annotation from the http://www.scandb.org/ , The SCAN website , and from data I got from my advisor

the Scan annotation as follows

snp chr pos
rs987435    7   78437519
rs345783    15  31183071
rs6088791   20  33371323
rs11180435  12  73950313
rs2342723   16  5688792

My data annotation is

snp chr pos
rs987435 chr7 78599583
rs345783 chr15 33395779
rs6088791 chr20 33907909
rs11180435 chr12 75664046
rs2342723 chr16 5748791

the position is different , why? which one shall I trust?

Thank you,

snp • 293 views
ADD COMMENTlink modified 9 months ago by pfs250 • written 9 months ago by mms14013050
2
gravatar for pfs
9 months ago by
pfs250
USA/Boston
pfs250 wrote:

Trust your data annotation. When you look up one SNP in dnSNP you will see that your annotation matches GRCh37 while the Scan annotation does not match GRCh38. https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=987435

Judging by data sources of information documented in the about SCAN link I am guessing that SNPs are mapped to an ever older version. http://www.scandb.org/newinterface/help.html

ADD COMMENTlink written 9 months ago by pfs250
2
gravatar for ATpoint
9 months ago by
ATpoint5.7k
Germany
ATpoint5.7k wrote:

Probably different genome assemblies. Scandb uses dbSNP129 from 2008, so the assembly is probably hg18. Your coordinates are hg19. You can use liftOver to check if that is true.

ADD COMMENTlink written 9 months ago by ATpoint5.7k
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