How to validate a ss and rs for SNPs?
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Entering edit mode
2.3 years ago
MichaelTrev ▴ 10

Hello, I have a many of SNP from SNPchimp base, and for example, in two files I have the same rs number, with the same position and same chromosome, but another ss.

Example: (chip_name, rs,ss,allels,orient, allels1, allels2, chromosome, positionOnChromosome)

Bov_IDBv2   rs17871566  ss28451907  A/G     forward     A/G     A/G     1   138583183


and:

Bov_IlluHD  rs17871566  ss251326633     A/G     forward     A/G     A/G     1   138583183


I have to be sure that rs are the same, and this is not just a mistake. So I would like to check if both "ss" refer to the same "rs". Where can I check it? dbSNP worked before but now it's only for human snps (?) in my case its cow SNPs, but now it does not search for "ss". Can anyone help?

SNP • 640 views
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Entering edit mode
2.3 years ago

Each variant that is submitted to dbSNP is assigned a unique 'ss' number. In some cases, 2 or more submissions (and, thus, two or more ss numbers) will actually relate to the same variant. So, in such cases, we will have a single rs ID with multiple ss IDs.

Kevin