Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc

Question

[Floris Brenk]

Hi all,

I had a more general question about SNP positions. So the genome get update once every few years and probably soon there will be a new update. SNPs map to certain coordinates of a genome and these differ of course per genome, but do also the actual SNP positions changes? in a sense that first the SNP was mapping really close to a gene and in a newer genome not anymore? How stable are the relative SNP positions in a genome?

[Ashutosh Pandey]

The relative SNPs positions should be stable but the actual SNP position will change between different reference genome versions.

Answer 1

[Pierre Lindenbaum]

A large majority of the SNPs should be located in the same regions and their positions should be more and more reliable

But some SNPs have moved from one chromosomes to another chromosome between each build:

mysql> select S7.name,S7.chrom as 'hg17',S8.chrom  as 'hg18' ,S9.chrom as 'hg19' from hg17.snp125 as S7, hg18.snp128 as S8, hg19.snp135 as S9 where S7.name=S8.name and S8.name=S9.name and S7.chrom!=S8.chrom and S8.chrom!=S9.chrom and S7.chrom!=S9.chrom and S7.weight=1 and S8.weight=1 and S9.weight=1 and LOCATE('_',S9.chrom)=0 and LOCATE('_',S8.chrom)=0 and  LOCATE('_',S7.chrom)=0 ;

+------------+-------+-------+-------+
| name       | hg17  | hg18  | hg19  |
+------------+-------+-------+-------+
| rs1140484  | chr10 | chr1  | chr22 |
| rs1047714  | chr11 | chr3  | chr16 |
| rs4018482  | chr11 | chr3  | chr4  |
| rs28903697 | chr11 | chr2  | chr8  |
| rs3007048  | chr11 | chr14 | chr8  |
| rs2086493  | chr12 | chr11 | chr4  |
| rs2086492  | chr12 | chr11 | chr4  |
| rs3201132  | chr12 | chr10 | chr19 |
| rs3199753  | chr12 | chr10 | chr19 |
| rs574969   | chr12 | chr9  | chr14 |
| rs2091195  | chr13 | chr9  | chr8  |
| rs2201744  | chr15 | chr7  | chr21 |
| rs2916722  | chr15 | chr8  | chr14 |
| rs2091200  | chr15 | chr7  | chr3  |
| rs2091199  | chr15 | chr7  | chr3  |
| rs11555717 | chr16 | chr1  | chr19 |
| rs570755   | chr16 | chr21 | chr10 |
| rs634224   | chr16 | chr5  | chr21 |
| rs3753277  | chr18 | chr1  | chr4  |
| rs427122   | chr18 | chr15 | chr7  |
| rs11540125 | chr19 | chr16 | chr1  |
| rs11557870 | chr1  | chr16 | chr2  |
| rs11555619 | chr20 | chr4  | chr3  |
| rs1065295  | chr20 | chr3  | chr6  |
| rs3009299  | chr21 | chr4  | chr1  |
| rs2845238  | chr22 | chr14 | chr2  |
| rs9618875  | chr2  | chr22 | chr16 |
| rs525201   | chr2  | chr11 | chr7  |
| rs11553811 | chr2  | chr12 | chr19 |
| rs1645789  | chr2  | chr19 | chr1  |
(...)