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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs6580873          
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/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NG_008184.1:g.8375T>G
NM_002281.2:c.743G>T
NM_002281.3:c.743T>G
NP_002272.2:p.Leu248Arg
NT_029419.11:g.14825231A>C
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 ss89153034 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6580873 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
ss10709236BCM_SSAHASNP|chr12.NT_029419.10_14825231byFreqfwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac06/29/0310/25/06116Genomicunknown
ss12178198WI_SSAHASNP|chr12.NT_029419.10_14825231fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac07/04/0310/10/03116Genomicunknown
ss15670142SC_SNP|NT_029419.10_14825231fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/17/0311/22/03120Genomicunknown
ss16582226CSHL-HAPMAP|CSHL-HuAA-200402.chr12.NT_029419.10_14825231fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac02/17/0403/04/04120Genomicunknown
ss20876826SSAHASNP|WGSA-200403-chr12.chr12.NT_029419.10_14825231fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac03/19/0403/19/04121Genomicunknown
ss24342242PERLEGEN|afd4484377byFreqfwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac08/10/0409/13/04123Genomicunknown
ss66545985ILLUMINA|HumanHap300v1.1_rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/09/0611/09/06127Genomicunknown
ss67475308ILLUMINA|HumanHap550v1.1_rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/14/0611/14/06127Genomicunknown
ss67831171ILLUMINA|HumanHap650Yv1.0_rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/14/0611/14/06127Genomicunknown
ss69109124PERLEGEN|PGP04484377byFreqfwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac01/30/0703/31/08127Genomicunknown
ss70874820ILLUMINA|HumanHap550v3.0__rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac04/20/0703/31/08130Genomicunknown
ss71464347ILLUMINA|HumanHap650Yv3.0_rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac04/23/0704/23/07127Genomicunknown
ss74806728AFFY|SNP_M-176884fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac08/09/0708/09/07128Genomicunknown
ss75486962ILLUMINA|ILMN_Human_1M_rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac08/28/0708/29/07129Genomicunknown
ss77705452HGSV|Cor12156_SNV_20070510.chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac10/09/0710/14/07129Genomicunknown
ss78611923HGSV|Cor12878_SNV_20070510.chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac10/17/0710/20/07129Genomicunknown
ss79226912ILLUMINA|HumanHap300v2.0_rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac04/18/0711/18/07130Genomicunknown
ss80446149HGSV|Cor18507_SNV_20070510.chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/23/0711/25/07130Genomicunknown
ss83888835HGSV|Cor18555_SNV_20070510.chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/27/0712/06/07130Genomicunknown
ss84509092KRIBB_YJKIM|KHS729618fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac12/04/0712/07/07130Genomicunknown
ss84739111HGSV|Cor19240_SNV_20070510.chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/30/0712/07/07130Genomicunknown
ss85964071HGSV|Cor18956_SNV_20070510.chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac11/30/0712/10/07130Genomicunknown
ss89153034BCMHGSC_JDW|JWB-0559673fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac02/26/0802/28/08129Genomicunknown
ss97229496HUMANGENOME_JCVI|1103649442072fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac03/28/0803/28/08130Genomicunknown
ss106806404BGI|BGI_rs6580873fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac09/16/0809/18/08130Genomicunknown
ss1135449981000GENOMES|NA19240_2008_12_16_2459687_chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac12/18/0812/18/08130Genomicunknown
ss118806858ILLUMINA-UK|NA18507_000066907_NCBI36.1_chr12_50968192fwd/TA/Cgaggtgtctgagatgtgcgactggagaatgggatctcctgcaggaggtgagggcagtgac01/21/0901/21/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6580873|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 GACCAGCATC CCCAGAAAAG GAAGCCTATT TAATAGATAT CTCACATCCC TCCCACTGAC
 ACGTCTAGCA GGCAGGTGTC CTGTGCCACT CACCTTGCTG CGGTACCAGG ACTCGGCCTC
 GGCCCGGCTG CGGGTGACAA TGTCGTCATA CTGTGCCTTA ATCTCGGCAA TGATGCAGTC
 CATGTTCAGG TCCCGGCTGT TGTCCAGCTT GACAACCACG GAGGTGTCTG AGATGTGCGA
 CTGGAGAATG
 M
 GGATCTCCTG CAGGAGGTGA GGGCAGTGAC TTTAGTTGAG AATACAGCCC CACCCACCAT
 GTCCTGACTC CACCTCCTCA GGCTTTCTCT GGTCCCCAAC CCTGCCCCCT CACACAGCCT
 CAGGGACTGC AACCTCTACC CACATCCTGT CCAACACTCC CACCCCCAAC TCTCCTCTCT
 GCTGGCTGCC AGGTTTCTGT CTGGCCCCTG AGCCCGCACC TCCTCATACA GCCGCCTCAG
 GAAGTCGATC

  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_029419 ABBA01031630
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/C
 C/C
 HWP A
 C
ss10709236 HapMap-CEU European 120 IG 0.300 0.700 0.200 0.150 0.850
HapMap-HCB Asian 88 IG 1.000 1.000
HapMap-JPT Asian 88 IG 0.023 0.977 1.000 0.011 0.989
HapMap-YRI Sub-Saharan African 120 IG 0.017 0.983 1.000 0.008 0.992
ss24342242 AFD_EUR_PANEL European 48 IG 0.208 0.792 0.584 0.104 0.896
AFD_AFR_PANEL African American 46 IG 0.174 0.826 0.655 0.087 0.913
AFD_CHN_PANEL Asian 48 IG 0.083 0.917 1.000 0.042 0.958
ss69109124 HapMap-CEU European 120 GF 0.300 0.700 0.150 0.850
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 0.022 0.978 0.011 0.989
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000
Concordant Genotype Total Sample A/C C/C
ss24342242 71 11 60
ss69109124 269 24 245
ss89153034 1121 119 895
ss97229496 1 1
RefSNP Genotype Summary Total Individual A/C C/C
rs6580873 1179 130 955
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5303 ss69109124 C/C CSHL-HAPMAP HapMap-YRI NA19141 YOR071.03 chr12-HapMap-YRI
5303 ss89153034 A/C CSHL-HAPMAP HapMap-YRI NA19141 YOR071.03 r27_ch12_YRI_bcm:genotype_0002
Genotype data submitted for1194 samples from1179 individualsIndividual with multiple genotypes submission:276

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .