Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2007 35(Database issue):D711-D715; doi:10.1093/nar/gkl962
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Nucleic Acids Research, 2007, Vol. 35, Database issue D711-D715
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms
1 Korean BioInformation Center, KRIBB Daejeon 305-806, Korea 2 Department of BioSystems, KAIST Daejeon 305-701, Korea 3 Department of Biology, Kyungpook National University Taegu 702-701, Korea 4 Department of Applied Statistics, Yonsei University 134, Shinchon-dong, Seodaemoon-gu, Seoul, Korea
*To whom correspondence should be addressed. Tel: +82 42 879 8531; Fax: +82 42 879 8519; Email: pj518{at}kribb.re.kr
Received August 15, 2006. Revised October 24, 2006. Accepted October 25, 2006.
Inherited genetic variation plays a critical but largely uncharacterized role in human differentiation. The completion of the International HapMap Project makes it possible to identify loci that may cause human differentiation. We have devised an approach to find such ethnically variant single-nucleotide polymorphisms (ESNPs) from the genotype profile of the populations included in the International HapMap database. We selected ESNPs using the nearest shrunken centroid method (NSCM), and performed multiple tests for genetic heterogeneity and frequency spectrum on genes having ESNPs. The function and disease association of the selected SNPs were also annotated. This resulted in the identification of 100 736 SNPs that appeared uniquely in each ethnic group. Of these SNPs, 1009 were within disease-associated genes, and 85 were predicted as damaging using the Sorting Intolerant From Tolerant system. This study resulted in the creation of the SNP@Ethnos database, which is designed to make this type of detailed genetic variation approach available to a wider range of researchers. SNP@Ethnos is a public database of ESNPs with annotation information that currently contains 100 736 ESNPs from 10 138 genes, and can be accessed at http://variome.net and http://bioportal.net/ or directly at http://bioportal.kobic.re.kr/SNPatETHNIC/.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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