Y-SNP indexes

This page provides information about the availability of indexes to Y-chromosome single nucleotide polymorphisms (Y-SNPs).

Integrated Y-SNP indexes

• YBrowse is maintained by Thomas Krahn and effectively serves as a master SNP index. As of January 2022 it holds over two million Y-SNP names and position information. YBrowse includes all the FGC, BY, FT, FTA, FTB, FTC and A SNPs but does not yet include the experimental FTT SNPs. YBrowse provides extracts of its database in various formats under the "Raw Data" link in the upper right of the main YBrowse page. The master index file is called snps_hg38.csv and is updated about two or three times a week. SNPs can be submitted to YBrowse using the template for bulk YBrowse uploads. To search for a SNP at YBrowse use the search bar where it says Landmark or Region. Type in the SNP you want to search without the base haplogroup letter (eg, for R-P312 type in P312). Hit Search to locate the relevant page for the SNP in the index. If you scroll down and click on the SNP name you are taken to another page with further details about the SNP including a list of all the alternative SNP names if applicable. If the SNP is found on YFull click on the SNP name under yfull_node and you will be taken to the relevant section of the YFull tree.
• The ISOGG SNP index is maintained by Ray Banks. Only SNPs which meet the listing criteria for inclusion on the ISOGG Y-SNP tree are included in this index. The ISOGG SNP index has not been updated since July 2020.
• Genetic Homeland DNA Marker Index. A free resource from Brad Larkin which provides an index of markers and their RSID positions on all 23 chromosomes.

Company Y-SNP indexes

In addition to the above indexes various companies maintain their own internal Y-SNP indexes. There is likely to be some overlap with these indexes and names found in one company's index will appear with a different name in another index. The YSEQ A-prefix SNPs are all in YBrowse.

• The BY SNP index which names SNPs discovered through early FamilyTreeDNA BigY testing (now superseded by the FT SNP index.
• The FGC SNP index which names SNPs discovered by Full Genomes Corporation
• The FT SNP index which “lists Big Y-700 SNPs that have been named by FamilyTreeDNA as they have been considered for inclusion to the Y chromosome haplotree. It supersedes the BY SNP index.
• The FTT SNP index. This lists ‘experimental SNPs discovered by realigning next generation sequencing data to the Telomere-to-Telomere (T2T) consortium's complete (but still work-in-progress) assembly of a human Y chromosome from NA24385, an Ashkenazi male belonging to Y-DNA haplogroup J1-M267'.
• The YFull SNP list. YFull SNPs have the prefixes Y and YP series. They are not all included in YBrowse.

Resources

• For a list of SNP prefixes see the ISOGG Y-SNP tree.
• The SNP Advanced Search Builder in the NCBI's dbSNP database can be used to determine the rsID (Reference SNP identification) for a particular Y-SNP, the rsID naming history (if any), as well as the flanking alleles and the correspondent position (at least for now) under GRCh37.

See also

• Y-DNA tools
• Y-SNP testing