Human Genome Diversity Project SNP Population Allele Frequencies (rs4940595)
  HGDP Selection Browser: rs4940595
Item: rs4940595
Position: chr18:59530818-59530818
Band: 18q21.33
Genomic Size: 1
View DNA for this feature (hg18/Human)
Ancestral Allele: T
Derived Allele: G

Ancestral Allele Frequencies for rs4940595:
Adygei0.6471
Balochi0.4583
BantuKenya0.3182
BantuSouthAfrica0.4375
Basque0.6250
Bedouin0.6000
BiakaPygmy0.5682
Brahui0.5600
Burusho0.5400
Cambodian0.4000
Colombian0.0714
Dai0.4500
Daur0.3889
Druze0.6905
French0.7321
Han0.5294
Han-NChina0.3500
Hazara0.5455
Hezhen0.5556
Italian0.8750
Japanese0.4464
Kalash0.6957
Karitiana0.6538
Lahu0.3125
Makrani0.5600
Mandenka0.4773
Maya0.3810
MbutiPygmy0.2692
Melanesian0.4091
Miao0.1500
Mongola0.3500
Mozabite0.6481
Naxi0.1250
Orcadian0.7667
Oroqen0.3889
Palestinian0.6848
Papuan0.2353
Pathan0.5455
Pima0.2143
Russian0.5200
San0.6000
Sardinian0.8393
She0.3000
Sindhi0.6042
Surui0.1250
Tu0.3000
Tujia0.3000
Tuscan0.7143
Uygur0.2500
Xibo0.6111
Yakut0.3800
Yi0.3500
Yoruba0.3810

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Population key: PDF  EPS  PNG
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Data last updated: 2010-09-15

Description

This track shows the 657,000 SNPs genotyped in 53 populations worldwide by the Human Genome Diversity Project in collaboration with the Centre d'Etude du Polymorphisme Humain (HGDP-CEPH). This track and several others are available from the HGDP Selection Browser.

Methods

Samples collected by the HGDP-CEPH from 1,043 individuals from around the world were genotyped for 657,000 SNPs at Stanford. Ancestral states for all SNPs were estimated using whole genome human-chimpanzee alignments from the UCSC database. For each SNP in the human genome (NCBI Build 35, UCSC database hg17), the allele at the corresponding position in the chimp genome (Build 2 version 1, UCSC database pantro2) was used as ancestral.

Allele frequencies were plotted on a world map using programs included in the Generic Mapping Tools.

Credits

Thanks to the HGDP-CEPH, the Pritchard lab at Stanford University, Joe Pickrell and John Novembre for sharing the data and plotting scripts for this track.

References

Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A et al. A human genome diversity cell line panel. Science. 2002 Apr 12;296(5566):261-2. PMID: 11954565

Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008 Feb 22;319(5866):1100-4. PMID: 18292342

Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW et al. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 2009 May;19(5):826-37. PMID: 19307593; PMC: PMC2675971

Wessel P, Smith WHF. New, improved version of Generic Mapping Tools released. EOS, Trans. Amer. Geophys. U. 1998;79(47):579.