Mapping SNPs with just position from ATG on gene

Question

[viavialin]

I'm trying to annotate the SNPs (ie. the rs# and chromosome position) from this Table 1 in this paper but am having difficulty locating the SNPs on the gene.

This table describes the position of each SNP from the ATG and I have identified the ATG to be chr3:183,732,180 (GRCh37) for NM_005688. Since this gene is in the reverse strand, I have added and subtracted the positions according.

However when entering the putative chromosome position of each SNP, it does not come up as a SNP in the UCSC browser (ie. no SNPs are identified)

Am I miscalculating the chromosome positions of the SNPs? Or has there been a change of chromosome position for this gene since 2003 (year of the paper)?

Answer 1

[Devon Ryan]

2003 was a few versions of the genome ago, so those positions are unlikely to be the same. Just look things up by rs ID in dbSNP.

[viavialin]

Unfortunately, I do not have the rs IDs! In fact, I am trying to identify the rs# from this paper..

[Devon Ryan]

Ah, I misread your post. You might try switching the version of the genome browser you're using. The UCSC genome browser goes back to hg16 and you can also download the reference sequence from UCSC of all the versions going back to hg1. Note that new versions were getting released every couple months back then, so you might have to check a few of them until you find the right one. For converting positions to the newest release you can use liftOver.

[viavialin]

Thanks for the suggestion, I eventually remapped the coordinates on the old version hg16 and used Kaviar to identify closest SNPs based on my converted input coordinates.