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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1125488          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_176891.3:c.137A>C
NM_176891.3:c.138A>C
NP_795372.1:p.Gln46His
NP_795372.1:p.Gln46Pro
NT_008413.17:g.21471556T>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 ss1479442 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1125488 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
ss1479442TSC-CSHL|TSC0098103byFreqfwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac09/07/0005/17/0486Genomic95 %
ss24296953PERLEGEN|afd0852576byFreqrev/BG/Tgtgtggtagacactgctgaattgacaaggttgcaacttattcaagagttttaaactttct08/10/0409/13/04123Genomicunknown
ss43845316ABI|hCV7574819rev/BG/Tgtgtggtagacactgctgaattgacaaggttgcaacttattcaagagttttaaactttct07/18/0507/18/05126Genomicunknown
ss66603383ILLUMINA|HumanHap300v1.1_rs1125488fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac11/09/0611/09/06127Genomicunknown
ss66929534ILLUMINA|HumanHap550v1.1_rs1125488fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac11/14/0611/14/06127Genomicunknown
ss67086316ILLUMINA|HumanHap650Yv1.0_rs1125488fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac11/14/0611/14/06127Genomicunknown
ss69286071PERLEGEN|PGP00852576byFreqrev/BG/Tgtgtggtagacactgctgaattgacaaggttgcaacttattcaagagttttaaactttct01/30/0708/14/07127Genomicunknown
ss70393172ILLUMINA|HumanHap300v2.0_rs1125488fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac04/18/0711/18/07127Genomicunknown
ss70527520ILLUMINA|HumanHap550v3.0__rs1125488rev/BG/Tgtgtggtagacactgctgaattgacaaggttgcaacttattcaagagttttaaactttct04/20/0703/30/08130Genomicunknown
ss71057694ILLUMINA|HumanHap650Yv3.0_rs1125488fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac04/23/0704/23/07127Genomicunknown
ss74810970AFFY|SNP_M-184688fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac08/09/0708/09/07128Genomicunknown
ss75437677ILLUMINA|ILMN_Human_1M_rs1125488fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac08/28/0708/29/07129Genomicunknown
ss83686133KRIBB_YJKIM|KHS519234fwd/TA/Cagaaagtttaaaactcttgaataagttgcaaccttgtcaattcagcagtgtctaccacac12/04/0712/05/07130Genomicunknown
ss1086692571000GENOMES|CEU.trio.12.15.2008_2151518_chr9_21471556rev/BG/Tgtgtggtagacactgctgaattgacaaggttgcaacttattcaagagttttaaactttct12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1125488|allelePos=196|totalLen=1229|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 CTATTTCTGG AATTTCCCTA AGTCTATGCA GGGATAAGTA GCATATTTGA CCTTCACCAT
 GATTATCAAG CACTTCTTTG GAACTGTGTT GGTGCTGCTG GCCTCTACCA CTATCTTCTC
 TCTAGATTTG AAACTGATTA TCTTCCAGCA AAGACAAGTG AATCAAGAAA GTTTAAAACT
 CTTGAATAAG TTGCA
 M
 ACCTTGTCAA TTCAGCAGTG TCTACCACAC AGGAAAAACT TTCTGCTTCC TCAGAAGTCT
 TTGAGTCCTC AGCAGTACCA AAAAGGACAC ACTCTGGCCA TTCTCCATGA GATGCTTCAG
 CAGATCTTCA GCCTCTTCAG GGCAAATATT TCTCTGGATG GTTGGGAGGA AAACCACACG
 GAGAAATTCC TCATTCAACT TCATCAACAG CTAGAATACC TAGAAGCACT CATGGGACTG
 GAAGCAGAGA AGCTAAGTGG TACTTTGGGT AGTGATAACC TTAGATTACA AGTTAAAATG
 TACTTCCGAA GGATCCATGA TTACCTGGAA AACCAGGACT ACAGCACCTG TGCCTGGGCC
 ATTGTCCAAG TAGAAATCAG CCGATGTCTG TTCTTTGTGT TCAGTCTCAC AGAAAAACTG
 AGCAAACAAG GAAGACCCTT GAACGACATG AAGCAAGAGC TTACTACAGA GTTTAGAAGC
 CCGAGGTAGG TGGAGGGACT AGAGGACTTC TCCAGACATG ATTCTTCATA GAGTGGTAAT
 ACAATTTATA GTACAATCAC ATTGCTTTGA TTTTGTGTAT ATATATATTT ATCTGTGTTT
 TAAGATTGTG CATATTGACC ACAATTGTTT TTATTTTGTA ATGTGGCTTT ATATATTCTA
 TCCATTTTAA ATTGTTTGTA TGTCAAAATA AATTCATTAA TATGGTTGAT TCTTCAAATG
 GGTGTATTTT CATACAGGCT GGCTGGGTAG ATACAATAAA ATATGCCACT AATGTAAAAA
 TACTTTCCTT AACATAGAAC TCCATTGCAA TGATTTGCTT ATTTGCCAGA AATTGCTAGA
 GACAATGAGA AATATTGGGA ATAATTTGCA TTTTAAGATT TGAAAATATT ATTACACAGT
 GAATATTTAC ATTACAGGAG ACAGAATAGA AATATGGTGA AAGGACATGA ACAGTTTGCA
 GAGAAAAAAA ACTACATTAA AAAAGGTTCA ATCTCACTCA AGAGAAAGGG TTTCTTNTTT
 NCCGCCACCT TAC

  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
NC_000009.9
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/C
 C/C
 HWP A
 C
ss1479442 HapMap-CEU European 120 IG 0.883 0.117 0.655 0.942 0.058
HapMap-HCB Asian 90 IG 0.978 0.022 1.000 0.989 0.011
HapMap-JPT Asian 88 IG 0.955 0.045 1.000 0.977 0.023
HapMap-YRI Sub-Saharan African 120 IG 0.950 0.050 1.000 0.975 0.025
ss24296953 AFD_EUR_PANEL European 46 IG 0.913 0.087 1.000 0.957 0.043
AFD_AFR_PANEL African American 46 IG 1.000 1.000
AFD_CHN_PANEL Asian 38 IG 1.000 1.000
ss69286071 HapMap-CEU European 120 GF 0.867 0.017 0.117 0.875 0.125
HapMap-HCB Asian 90 GF 0.978 0.022 0.978 0.022
HapMap-JPT Asian 90 GF 0.956 0.044 0.956 0.044
HapMap-YRI Sub-Saharan African 120 GF 0.950 0.050 0.950 0.050
Concordant Genotype Total Sample A/A A/C C/C
ss1479442 1189 1084 82 2
ss24296953 71
RefSNP Genotype Summary Total Individual A/A A/C C/C
rs1125488 1263 1084 82 2
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
160 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA12239 CEPH1334.13 r27_ch9_CEU_illumina:human_1m_beadchip 684462
172 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA07056 CEPH1340.12 r27_ch9_CEU_illumina:human_1m_beadchip 684462
174 ss1479442 N/N CSHL-HAPMAP HapMap-CEU NA07048 CEPH1341.01 r27_ch9_CEU_illumina:human_1m_beadchip 684462
184 ss1479442 N/N CSHL-HAPMAP HapMap-CEU NA07034 CEPH1341.11 r27_ch9_CEU_illumina:human_1m_beadchip 684462
363 ss1479442 A/A CSHL-HAPMAP HapMap-CEU NA11995 CEPH1362.16 r27_ch9_CEU_illumina:human_1m_beadchip 684462
546 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA12761 CEPH1447.10 r27_ch9_CEU_illumina:human_1m_beadchip 684462
579 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA12815 CEPH1454.15 r27_ch9_CEU_illumina:human_1m_beadchip 684462
610 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA12864 CEPH1459.01 r27_ch9_CEU_illumina:human_1m_beadchip 684462
619 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA12873 CEPH1459.10 r27_ch9_CEU_illumina:human_1m_beadchip 684462
623 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA12878 CEPH1463.02 r27_ch9_CEU_illumina:human_1m_beadchip 684462
637 ss1479442 A/C CSHL-HAPMAP HapMap-CEU NA12892 CEPH1463.16 r27_ch9_CEU_illumina:human_1m_beadchip 684462
5144 ss1479442 A/C CSHL-HAPMAP HapMap-YRI NA19192 YOR112.03 r27_ch9_YRI_illumina:human_1m_beadchip 684462
5192 ss1479442 A/C CSHL-HAPMAP HapMap-HCB NA18637 CH18637 r27_ch9_CHB_illumina:human_1m_beadchip 684462
5224 ss1479442 A/C CSHL-HAPMAP HapMap-JPT NA18974 JA18974 r27_ch9_JPT_illumina:human_1m_beadchip 684462
5225 ss1479442 A/C CSHL-HAPMAP HapMap-JPT NA18987 JA18987 r27_ch9_JPT_illumina:human_1m_beadchip 684462
5304 ss1479442 A/C CSHL-HAPMAP HapMap-YRI NA19154 YOR072.01 r27_ch9_YRI_illumina:human_1m_beadchip 684462
5306 ss1479442 A/C CSHL-HAPMAP HapMap-YRI NA19153 YOR072.03 r27_ch9_YRI_illumina:human_1m_beadchip 684462
5309 ss1479442 A/C CSHL-HAPMAP HapMap-YRI NA19144 YOR074.03 r27_ch9_YRI_illumina:human_1m_beadchip 684462
Genotype data submitted for1278 samples from1263 individualsIndividual with multiple genotypes submission:15

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .