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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2020870          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:94/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_001460.2:c.107A>G
NP_001451.1:p.Asp36Gly
NT_004487.18:g.21645314A>G
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss105440113 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2020870 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss2923974UWGC|fmo2-e2+t26byFreqfwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag09/07/0104/07/04101Genomicunknown
ss3188954HGBASE|SNP000064461fwd/TA/Gcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaa07/23/0110/10/0398cDNAunknown
ss9901144BCM_SSAHASNP|chr1.NT_004487.15_8518byFreqfwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag06/27/0304/07/04116Genomicunknown
ss35038969EGP_SNPS|FMO2-002515byFreqfwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag02/28/0511/02/06125Genomicunknown
ss65730888ILLUMINA|Human1-rs2020870fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag10/10/0610/10/06127Genomicunknown
ss66610491ILLUMINA|HumanHap300v1.1_rs2020870fwd/BA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag11/09/0611/09/06127Genomicunknown
ss67215908ILLUMINA|HumanHap550v1.1_rs2020870fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag11/14/0611/14/06127Genomicunknown
ss67609641ILLUMINA|HumanHap650Yv1.0_rs2020870fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag11/14/0611/14/06127Genomicunknown
ss68784589PERLEGEN|PGP00659605byFreqfwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag01/30/0708/14/07127Genomicunknown
ss70694171ILLUMINA|HumanHap550v3.0__rs2020870rev/BC/Tcttactttgaacctccacactcctccaatacttcagttctctcaaagcaagtgggctcaa04/20/0703/30/08130Genomicunknown
ss71259513ILLUMINA|HumanHap650Yv3.0_rs2020870fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag04/23/0704/23/07127Genomicunknown
ss74809259AFFY|SNP_M-181877fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag08/09/0708/09/07128Genomicunknown
ss75445549ILLUMINA|ILMN_Human_1M_rs2020870fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag08/28/0708/29/07129Genomicunknown
ss79107815ILLUMINA|HumanHap300v2.0_rs2020870fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag04/18/0711/18/07130Genomicunknown
ss83945908KRIBB_YJKIM|KHS580453fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag12/04/0712/06/07130Genomicunknown
ss84154427PHARMGKB_AB_DME|PS206247_PA150293634_301fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag12/06/0712/10/07130Genomicunknown
ss105440113SNP500CANCER|FMO2-17fwd/TA/Gttgagcccacttgctttgagagaactgaagtattggaggagtgtggaggttcaaagtaag09/05/0809/05/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2020870|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CCATAAGAAA CTCAGCTTTT CTCAAAGGCA AGAAGAGAGC AGGATTTTTG ACTGGCTCTT
 TATTCAATAG TGCTGCTTAT TAAATTACCA CTGCTACAAT GTTTAAAGCC AATTACCTGA
 GCACATCATA AGGATTCTCT TACCGGTTGT CCCAGTTAAG TAATGTTGAT TGATCAACTC
 CTTGACAGGA GCTGATGGCA AAGAAGGTAG CTGTGATTGG AGCTGGGGTC AGTGGCCTAA
 TTTCTCTGAA GTGCTGTGTG GATGAGGGAC TTGAGCCCAC TTGCTTTGAG AGAACTGAAG
 R
 TATTGGAGGA GTGTGGAGGT TCAAAGTAAG TGAGATTTTC TTGGGTCTTG AACAGGTTGT
 GTTGTTATTT CARGGTGAAT CACAGTTACT GATGGGTCAT ATTGAGAAAT TTATTAAACA
 ACTCTGATCA GATTTTATTT CTAYTTATTG ATGTGGCCAT AATGGAACTG AAGTCATAGG
 CTGGCATCTC TCCCCCAGTC AATACTAACC CAACCCAGGT AGCTGACCCA GGCATGTAAA
 AGATCTCTTC TTTTGGATTC AGCAATTGTC TTACAGCCCA TACTTCTGTC ATTCTTTAAT

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_004487
dbSNP Blast Analysis
UniGene Cluster ID
144912

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss105440113 P1 204 GF 0.833 0.157 0.010 0.912 0.088
CAUC1 62 GF 0.903 0.097 0.952 0.048
AFR1 48 GF 0.833 0.167 0.917 0.083
HISP1 46 GF 0.826 0.130 0.043 0.891 0.109
PAC1 48 GF 0.750 0.250 0.875 0.125
P2 398 GF 0.819 0.166 0.015 0.902 0.098
CAUC2 114 GF 0.930 0.070 0.965 0.035
AFR2 112 GF 0.804 0.196 0.902 0.098
P3 556 GF 0.881 0.101 0.018 0.932 0.068
CAUC3 132 GF 0.848 0.121 0.030 0.909 0.091
AFR3 150 GF 0.893 0.093 0.013 0.940 0.060
HISP3 98 GF 1.000 1.000
PAC3 176 GF 0.830 0.148 0.023 0.903 0.097
ASI2 172 GF 0.756 0.209 0.035 0.860 0.140
ss2923974 NIHPDR Global 84 IG 0.881 0.119 0.752 0.940 0.060
ss35038969 HapMap-CEU European 120 IG 0.933 0.067 1.000 0.967 0.033
HapMap-HCB Asian 90 IG 0.778 0.178 0.044 0.150 0.867 0.133
HapMap-JPT Asian 88 IG 0.750 0.227 0.023 1.000 0.864 0.136
HapMap-YRI Sub-Saharan African 120 IG 0.800 0.200 0.403 0.900 0.100
EGP_YORUB-PANEL Sub-Saharan African 24 IG 0.833 0.167 1.000 0.917 0.083
EGP_HISP-PANEL Hispanic 42 IG 0.762 0.238 0.584 0.881 0.119
EGP_CEPH-PANEL European 44 IG 0.909 0.091 1.000 0.955 0.045
EGP_AD-PANEL African American 28 IG 1.000 1.000
EGP_ASIAN-PANEL Asian 48 IG 0.708 0.250 0.042 0.655 0.833 0.167
ss68784589 HapMap-CEU European 120 GF 0.933 0.067 0.967 0.033
HapMap-HCB Asian 90 GF 0.778 0.178 0.044 0.867 0.133
HapMap-JPT Asian 90 GF 0.756 0.222 0.022 0.867 0.133
HapMap-YRI Sub-Saharan African 120 GF 0.800 0.200 0.900 0.100
ss84154427 PA150293635 356 AF 0.896 0.104
ss9901144 CEPH 184 AF 0.920 0.080

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.156+/-0.232 1286 1081 270 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwithHapMapFreq
Validated by: PERLEGEN
 UNKNOWN UNKNOWN YES

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Revised: May 25, 2006 1:38 PM .