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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs357503          
refSNP ID: rs357503
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_015595.2:c.2091-1347A>G
NT_005612.15:g.60451958A>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 ss1629404 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs357503 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
ss453753KWOK|OVLP-000621-384119rev/TA/Gattagaggaggtgagttggaaagaaaggcctgctggttagagagtggtatgtttgacact06/30/0010/10/0379Genomic99 %
ss608659SC_JCM|AC012341.3_143934fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat07/12/0010/10/0380Genomicunknown
ss1031523KWOK|OVLP-000804-419692fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat09/02/0010/10/03123Genomic97 %
ss1031793KWOK|OVLP-000804-423767fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat09/02/0010/10/0386Genomic97 %
ss1629404KWOK|OVLP-000925-60274byFreqfwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat10/04/0010/25/06123Genomic97 %
ss1629645KWOK|OVLP-000925-65627byFreqfwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat10/04/0005/16/0487Genomic97 %
ss14208232BCM_SSAHASNP|chr3.NT_005612.14_60451966rev/TA/Gattagaggaggtgagttggaaagaaaggcctgctggttagagagtggtatgtttgacact11/05/0311/22/03119Genomicunknown
ss41889286ABI|hCV8910280rev/TA/Gattagaggaggtgagttggaaagaaaggcctgctggttagagagtggtatgtttgacact07/17/0507/17/05126Genomicunknown
ss66165600AFFY|SNP_A-2178605byFreqfwd/BC/Tcactctctaaccagcaggcctttctttccaac10/27/0608/14/07127Genomicunknown
ss67296352ILLUMINA|HumanHap550v1.1_rs357503fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat11/14/0611/14/06127Genomicunknown
ss67700696ILLUMINA|HumanHap650Yv1.0_rs357503fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat11/14/0611/14/06127Genomicunknown
ss68219731ILLUMINA|HumanHap250Sv1.0_rs357503fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat12/06/0612/07/06127Genomicunknown
ss68879909PERLEGEN|PGP07153646byFreqrev/TA/Gattagaggaggtgagttggaaagaaaggcctgctggttagagagtggtatgtttgacact01/30/0708/14/07127Genomicunknown
ss70774976ILLUMINA|HumanHap550v3.0__rs357503rev/TA/Gattagaggaggtgagttggaaagaaaggcctgctggttagagagtggtatgtttgacact04/20/0703/30/08130Genomicunknown
ss71350860ILLUMINA|HumanHap650Yv3.0_rs357503fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat04/23/0704/23/07127Genomicunknown
ss75924543ILLUMINA|ILMN_Human_1M_rs357503fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat08/28/0708/29/07129Genomicunknown
ss76213420AFFY|AFFY_6_1M_SNP_A-2178605fwd/BC/Tcactctctaaccagcaggcctttctttccaac08/28/0708/30/07129Genomicunknown
ss82680408HGSV|Cor19240_SNV_20070510.chr3_155439510rev/TA/Gattagaggaggtgagttggaaagaaaggcctgctggttagagagtggtatgtttgacact11/30/0712/03/07130Genomicunknown
ss83437758KRIBB_YJKIM|KHS461609fwd/BC/Tagtgtcaaacataccactctctaaccagcaggcctttctttccaactcacctcctctaat12/04/0712/05/07130Genomicunknown
ss92333885BCMHGSC_JDW|JWB-1685411rev/TA/Gattagaggaggtgagttggaaagaaaggcctgctggttagagagtggtatgtttgacact02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs357503|allelePos=1040|totalLen=1527|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 ATGCATCTTG GTCATGCTCC AGCAGGTGTA CCTCCCCAGC TTCCACATCT CTATTTGCAG
 AATGAAGGAG GAGCCTTCTA CTCATGCTCT GGGTAACAAG ACCTCACCCC CCAAACCCCC
 CATCTCCAAA TGACCATGCA TTGAAGAGAA GAGCCCCAGA GGTCTGCTTG CTTCTGGCAA
 GACacccaac ccatccttgt gtcccacact cagagcctca ccacctgttt cacaaaccac
 caggactaat ctcattatgc cctccattcc tgcttaggct caggaacccc aatatccttc
 tttctcctgc actcccattc ccatcgcact gtgaacatgc ccaatctggc cccacttttt
 tccactcctc agctggttcc tgaacccctt ccactgtacc ctctgggaat gcaattccct
 catttaagaa actagtaaag tcttctaaat acttggcctc gtctctgaac cctcccttca
 cattcttgcc ttaaaagaaa cctggctctc cctagagaac aaggcgtctc ctgagagctc
 tctgcctgct tgctttttat tcctgcttct atacaatgat cacttcctcc tcctgaaaca
 tcatcagctt tgaagctcat ggcatcagtc tctaactcat aactacagtc atctatagac
 ccctggatcg tttccgatcc tctcccttga gtttcactgc tggctctctg tctctctcca
 acaatacttc ttcatacaca cacacacaca cacacacaca cacactctct ctctctctct
 ctctctctct ctctctctct ctccctctct ctcggtcatt tacatcaagt ccccaacact
 acttctttct tgaagtctcc tgtaaaggat ctttccatta ccctgtaccc tcaattcccc
 gactttactc tcctccgatg atcttgtttt ctgccctact tcagccacaa atccatggtt
 ataccttagt ccttgtcatt accatcaact acaacctctc tgtaatccca gtgtcaaaca
 taccactctc taaccagca
 Y
 ggcctttctt tccaactcac ctcctctaat cctcaacacc aaccattatt taactcacca
 gttcttacaa cccattgact ctacaacctt ccgcctcccc cccttaattc cctcatgtcc
 tcttgttcat gcatattaaa ttagctagct tgcatttctt ggtacccagt taaatcacat
 cttgcataca cattcatctc cttgattgta tttgcctggc aaatcccgaa cctggtgaca
 tacagctttt cctctactct gcacctgcac ccttgcgagt gaacatgAGA GTGCTCAATA
 AATAACTGTC ACATAAGTGG ATGAATATGC AATAAATTCT AATATACGCT AGGAATATCG
 AATAATTACC TCATTTAATA ATAAATGCAA ATGAATGATG TCAGGGGAGC TTAGAGAAAA
 GAAAACTCCT TGTGCCTAGT CCAGTACACT AGGAGGAATT TCAGAACAGG CCACTTTGCT
 CAAGATT

  GeneView back to top
GeneView via analysis of contig annotation: SGEF Src homology 3 domain-containing guanine nucleotide exchange factor
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_005612->NM_015595
function
HuRefNW_001838884->NM_015595
function
CeleraNW_921807->NM_015595
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_005612->NM_015595->NP_05641060451958forwardintron
HuRefNW_001838884->NM_015595->NP_05641040077436reverseintron
CeleraNW_921807->NM_015595->NP_05641060563171forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs357503 maps exactly once on NCBI human chromosome 3
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
3NW_001838884.240077436151351595plusTalt_assembly_8HuRefHuRefview1039
3NW_921807.160563171152377501minusGalt_assembly_1CeleraCeleraview1039
3NT_005612.1560451958155439502minusAref_assemblyreferencereferenceview1039

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005612 AC018452 AC018452.11 AC072034.10
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1629404HapMap-CEUEuropean 120IG 0.467 0.450 0.083 0.752 0.692 0.308
HapMap-HCBAsian 90IG 0.267 0.600 0.133 0.150 0.567 0.433
HapMap-JPTAsian 88IG 0.409 0.477 0.114 0.648 0.352
HapMap-YRISub-Saharan African 114IG 0.368 0.421 0.211 0.317 0.579 0.421
ss1629645CEPH 184AF 0.100 0.900
ss66165600HapMap-CEUEuropean 118GF 0.458 0.458 0.085 0.686 0.314
HapMap-HCBAsian 90GF 0.267 0.600 0.133 0.567 0.433
HapMap-JPTAsian 90GF 0.422 0.467 0.111 0.656 0.344
HapMap-YRISub-Saharan African 120GF 0.350 0.417 0.233 0.558 0.442
ss68879909HapMap-CEUEuropean 120GF 0.467 0.450 0.083 0.692 0.308
HapMap-HCBAsian 90GF 0.267 0.600 0.133 0.567 0.433
HapMap-JPTAsian 90GF 0.422 0.467 0.111 0.656 0.344
HapMap-YRISub-Saharan African 120GF 0.350 0.417 0.233 0.558 0.442

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.471+/-0.1162702102700

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .