Y-DNA SNP Index on Spreadsheet - 2016

The entire work is identified by the Version Number and date given on the Main Page.   Directions for citing the document are given at the bottom of the Main Page.
Version History     Last revision date for this specific page: 5 December 2016
Email Ray Banks if you find any broken links on this page.

LINKS:  Main Page   Y-DNA Tree Trunk   Papers/Presentations Cited   Glossary   Listing Criteria

Contact person for SNP Index: Ray Banks

The ISOGG SNP Index web page lists the SNPs which are either on the ISOGG Y Haplotree or that are or have been under active investigation and consideration for addition to the Y Haplotree. The SNPs listed here are less than 20% of the currently known SNPs. A separate tab on the index spreadsheet contains known mutations from Denisovans.


EXPLANATION OF CONTENTS:

Explanation of SNPs with Extension Numbers.


The top of the spreadsheet has a link to YBrowse, which is primarily a listing of all known shared human Y-DNA variants maintained by Thomas Krahn. Only some of these are in the ISOGG tree. Some do not qualify. To do look-ups in YBrowse: In the Search Box under Landmark or Region on the left hand side of the page, you can type a SNP name such as M222, or a position such as chrY:14002414..14902414, then click on the Search button. When the search is complete, the SNP name appears under the Detail section. If you click on the SNP name in the Detail section, you will get a new window which shows the SNP mutations and other information.
Click here to open YBrowse directly.


RefSNP ID (aka rs numbers) are available on the spreadsheet for some of the ISOGG mutations. These are from the National Center for Biotechnology Information (NCBI) website. A more complete listing is available within YBrowse. Rs numbers can be further searched at the NCBI website, http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?/
References: NCBI, UCSC FAQ

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-> -> -> -> -> CLICK HERE TO VIEW THE INDEX (A GOOGLE SPREADSHEET)
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Note that a 2nd tab there has comparative Denisovan mutation information.
Use the link to YBrowse for updated rs-numbers (if any) and context on mutations.
Use the link to the NCBI database for more information on rs-number sites.
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Click here to view the April 21, 2016 version of the index which is the last containing long haplogroup names.


Additional Resources for identifying refSNP IDs
Brion et al, Introduction of a Single Nucleodite Polymorphism-based "Major Y-chromosome Haplogroup Typing Kit" Suitable for Predicting the Geographical Origin of Male Lineages. (abstract) Electrophoresis, 26:4411-4420, 2005.
Y Chromosome Consortium, A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups. Genome Research, 12: 339-348, 2002.

Not listed in Composite List of Papers Cited
The following documents are used simply to document the citation for particular SNPs.
Family Tree DNA (FTDNA) 2005 Y-Chromosome Phylogenetic Tree. Genealogy by Genetics, Ltd., 18 October 2004.
Shen et al, Population Genetic Implications from Sequence Variation in Four Y Chromosome Genes. PNAS, Vo. 97, No. 13: 7354-7359, June 20, 2000.

Corrections/Additions made since 1 January 2016:

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