Ucsc Snp Genomic Positions (Duplicates And Wrong Positions)

Question

[Panagiotis Alexiou]

I have a serious problem with UCSC SNP locations. Briefly:

I have downloaded from Tables => hg18, the table SNP130 as a bed file. This should have genomic locations of SNPs on human genome 18.

There are some SNPs that have multiple positions. I have read another question and I think this is because they fall on repeat elements.

However, I have also found at least one SNP (rs36164264) for which:

a. there are 2 genomic positions in the SNPs table

chr1 169314673 169314674 rs36164264 0 -
chr1 169333274 169333275 rs36164264 0 +

b. when searching for rs36164264 in UCSC hg18 Genome Browser it gives me back two different positions

snp130
rs36164264 at chr1:169314424-169314924
rs36164264 at chr1:169333025-169333525

c. when I follow the first link chr1:169314424-169314924 it takes me to a 500 nt long repeat element where there is no trace of the SNP (although there are other SNPs there).

d. when I follow the first location from the SNPs table chr1:169314673-169314674 it takes me to 1nt that is not annotated as the SNP in question.

I am utterly confused - hope for any insights and help.

Answer 1

[Pierre Lindenbaum]

• go in the genome browser
• click on "Variation and Repeats/Snp130" (SNPs (130) Track Settings)
• open "Filtering Options"
• set maximum Weight:3 ( Range: 1, 2 or 3; SNPs with higher weights are less reliable )
• submit

et voila,

you should see rs36164264 now.

[Panagiotis Alexiou]

This seems to solve the question of the missing SNP. Do you (or anyone) have any idea why the genomic intervals are different in the Tables and in the Genome Search?

[Pierre Lindenbaum]

The genome search just returns a large window surrounding the real position of the SNP