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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs6909298          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_032194.1:c.178G>A
NP_115570.1:p.Gly60Ser
NT_025741.14:g.15479681G>A
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 ss10287988 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6909298 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
ss10287988BCM_SSAHASNP|chr6.NT_025741.12_15479681byFreqfwd/TA/Ggttttacagtatgcactgaaaaaaccatacgtgtactatataaaaagtaagtcatgattt06/27/0310/25/06116Genomicunknown
ss68987754PERLEGEN|PGP04754027byFreqfwd/TA/Ggttttacagtatgcactgaaaaaaccatacgtgtactatataaaaagtaagtcatgattt01/30/0703/31/08127Genomicunknown
ss74821966AFFY|SNP_M-327086fwd/TA/Ggttttacagtatgcactgaaaaaaccatacgtgtactatataaaaagtaagtcatgattt08/09/0708/09/07128Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6909298|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=128
 AGAATATTAA GCTTACATTT CAAGTTACTG TAAGTGATGA AAAGGGAGCC AGGCAGAAGC
 CCTCAGAATA AGATTGAGGC CCCAGAGCAA TCTTGGAGAG TGACTGTTAT GATGCTTTAT
 TTTTATTTCT GCTTTTCAGA ATGTGTTTTG TTTTGAAAGC TATAAATTTT GTTTTACAGT
 ATGCACTGAA AAAACCATAC
 R
 GTGTACTATA TAAAAAGTAA GTCATGATTT CTTTTACTGT ATTTTAAATG ATTTTGTTTC
 ATTATAAAAG TAACCACTTT ATGGAAGATT TGGAAAACAA AAACTTTTTA AAAAGATATT
 AAAATTCCTT ACAGTTATTA ATATTTTAAT TTCTTTCTTT TGGTCTGTTT TTTTCATTTG
 TATTGAATGT CCTTGCATAG

  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_025741
dbSNP Blast Analysis
UniGene Cluster ID
372265

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/G
 G/G
 HWP A
 G
ss10287988 HapMap-CEU European 116 IG 1.000 1.000
HapMap-HCB Asian 88 IG 1.000 1.000
HapMap-JPT Asian 86 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 116 IG 0.207 0.793 1.000 0.103 0.897
ss68987754 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.217 0.783 0.108 0.892
Concordant Genotype Total Sample A/G G/G
ss10287988 519 10 247
ss68987754 264 10 254
RefSNP Genotype Summary Total Individual A/G G/G
rs6909298 525 10 254
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5139 ss10287988 A/G CSHL-HAPMAP HapMap-YRI NA19100 YOR105.01 r27_ch6_YRI_bcm:genotype_0002 3195852
5139 ss68987754 A/G CSHL-HAPMAP HapMap-YRI NA19100 YOR105.01 chr6-HapMap-YRI
5141 ss10287988 A/G CSHL-HAPMAP HapMap-YRI NA19098 YOR105.03 r27_ch6_YRI_bcm:genotype_0002 3195852
5141 ss68987754 A/G CSHL-HAPMAP HapMap-YRI NA19098 YOR105.03 chr6-HapMap-YRI
5270 ss10287988 A/G CSHL-HAPMAP HapMap-YRI NA19092 YOR040.03 r27_ch6_YRI_bcm:genotype_0002 3195852
5270 ss68987754 A/G CSHL-HAPMAP HapMap-YRI NA19092 YOR040.03 chr6-HapMap-YRI
5273 ss10287988 A/G CSHL-HAPMAP HapMap-YRI NA19101 YOR042.03 r27_ch6_YRI_bcm:genotype_0002 3195852
5273 ss68987754 A/G CSHL-HAPMAP HapMap-YRI NA19101 YOR042.03 chr6-HapMap-YRI
5278 ss10287988 A/G CSHL-HAPMAP HapMap-YRI NA19201 YOR045.02 r27_ch6_YRI_bcm:genotype_0002 3195852
5278 ss68987754 A/G CSHL-HAPMAP HapMap-YRI NA19201 YOR045.02 chr6-HapMap-YRI
5302 ss10287988 N/N CSHL-HAPMAP HapMap-YRI NA19140 YOR071.02 r27_ch6_YRI_bcm:genotype_0002 3195852
5302 ss68987754 A/G CSHL-HAPMAP HapMap-YRI NA19140 YOR071.02 chr6-HapMap-YRI
Genotype data submitted for525 samples from525 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .