SNPs that are merged in dbSNP

Question

[janhuang.cn]

I am analysing the 1000G VCF files, rs80314515 is not available in the VCF, but rs10204648 is available.

dbSNP returns this message when I search rs80314515 (https://www.ncbi.nlm.nih.gov/snp/?term=rs80314515)

rs80314515 has merged into rs10204648

I wonder if there is a data base about which SNPs are merged? (For all the SNPs currently known)

And another issue is chr:pos for rs10204648 is chr2:85882623 according to dbSNP, but it is on chr2:86109746. Any idea what could be the reason? Is it different build?

Answer 1

[Kevin Blighe]

Firstly, the discrepancy that you observe with the position on chr2 is due to different genome reference builds:

• chr2:85882623 = GRCh38 / hg38
• chr2:86109746 = GRCh37 / hg19

Merging of records FAQ

Yes, the merging of records is more common than you may imagine. There is a FAQ on the merging of dbSNP rs IDs here: https://www.ncbi.nlm.nih.gov/books/NBK44468/

All merged dbSNP records

In addition, here is a search configuration that lists all dbSNP rs IDs that have been merged: https://www.ncbi.nlm.nih.gov/snp/?term=mergedrs (the option to download the data is on that page - see 'Send to' at top-right).

Same dbSNP, multiple positions

You should also be aware that quite a few dbSNP rs IDs are duplicated and have different positions in the same reference genome build. Take a look at the reason here: https://www.ncbi.nlm.nih.gov/books/NBK44455/#Build.why_does_rs3823342_have_two_differ_1

Good luck and trust that this helps.

Kevin

[janhuang.cn]

Thank you very much.

[janhuang.cn]

Using the "Send to" function to download is very slow.

RsMergeArch.bcp.gz is available in the dbSNP FTP folder: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/