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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs961030          
refSNP ID: rs961030
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/129
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_030613.2:c.822A>G
NP_085116.2:p.Q274Q
NT_023133.12:g.23168721A>G
Links

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 ss48415801 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs961030 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
ss1407754TSC-CSHL|TSC0264602byFreqfwd/TA/Gtactggagaaaaaccctatgagtgtagtcatgtggaaaagcctttagtaagagctcaact09/06/0004/07/0486Genomic95 %
ss4919910YUSUKE|IMS-JST087633byFreqrev/BC/Tagttgagctcttactaaaggcttttccacatgactacactcatagggtttttctccagta07/24/0210/10/03108Genomicunknown
ss5836813SC_JCM|NT_006802.10_152128rev/BC/Tagttgagctcttactaaaggcttttccacatgactacactcatagggtttttctccagta01/10/0310/10/03111Genomicunknown
ss11720746WI_SSAHASNP|chr5.NT_077451.2_1454342fwd/TA/Gtactggagaaaaaccctatgagtgtagtcatgtggaaaagcctttagtaagagctcaact07/03/0310/10/03116Genomicunknown
ss24376024PERLEGEN|afd2601935byFreqfwd/TA/Gtactggagaaaaaccctatgagtgtagtcatgtggaaaagcctttagtaagagctcaact08/10/0409/13/04123Genomicunknown
ss48415801APPLERA_GI|hCV8294125byFreqrev/BC/Tagttgagctcttactaaaggcttttccacatgactacactcatagggtttttctccagta09/28/0511/03/06126Genomicunknown
ss68960976PERLEGEN|PGP02601935byFreqfwd/TA/Gtactggagaaaaaccctatgagtgtagtcatgtggaaaagcctttagtaagagctcaact01/30/0708/14/07127Genomicunknown
ss93354837BCMHGSC_JDW|JWB-2082081fwd/TA/Gtactggagaaaaaccctatgagtgtagtcatgtggaaaagcctttagtaagagctcaact02/26/0803/04/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs961030|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TGTCCATCAA CGAACTCACA CCGGAGAGAA ACCCTATCAG TGTAAAGAGT GTGGCAAAGC
 CTTCCATAAG AATTCATCTC TTATTCAGCA TGAAAGGATT CATACTGGAG AGAAACCCTA
 CAAATGTAAT GAATGTGGTA AAGCTTTTAC CCAAAGCATG AATTTGACAG TTCATCAGAG
 AACTCATACA GGAGAAAAAC CCTATGAATG TAATGAATGT GGAAAAGCCT TCAGTCAAAG
 CATGCATCTT ATTGTACATC AGAGAAGCCA TACTGGAGAA AAACCCTATG AGTGTAGTCA
 R
 TGTGGAAAAG CCTTTAGTAA GAGCTCAACT CTTACCCTAC ATCAGCGAAA TCACACTGGA
 GAAAAACCTT ACAAATGTAA CAAATGCGGG AAATCCTTTA GCCAAAGTAC ATATCTTATA
 GAACATCAGA GACTTCATTC TGGAGTAAAA CCTTTTGAAT GTAACGAGTG TGGAAAAGCT
 TTCAGTAAGA ATTCATCTCT AACTCAACAT CGGAGAATTC ACACTGGAGA GAAACCTTAT
 GAGTGTATGG TGTGTGGAAA ACATTTCACT GGACGATCAT CCCTTACCGT GCATCAGGTC

  GeneView back to top
GeneView via analysis of contig annotation: ZFP2 zinc finger protein 2 homolog (mouse)
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_023133->NM_030613
function
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_023133->NM_030613->NP_08511623168722forward1331synonymousGGln [Q]3274
contig referenceAGln [Q]3274

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs961030 maps exactly once on NCBI human chromosome 5
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
5NW_001838967.1890082173085750plusAalt_assembly_8HuRefHuRefview300
5NW_922818.1883965173986617plusAalt_assembly_1CeleraCeleraview300
5NT_023133.1223168722178291742plusAref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_077451
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank mRNA:
NM_030613.2 AK025281.1 AK131367.1 BC132779.1 BC132781.1 BC142989.1
UniGene Cluster ID
484328
3D structure mapping
NP_085116  

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss1407754CEPH 184AF 1.000
CHMJAsian 74IG 0.595 0.405
ss24376024AFD_EUR_PANELEuropean 46IG 0.435 0.391 0.174 0.479 0.630 0.370
AFD_AFR_PANELAfrican American 46IG 0.652 0.304 0.043 1.000 0.804 0.196
AFD_CHN_PANELAsian 48IG 0.583 0.292 0.125 0.200 0.729 0.271
ss48415801HapMap-CEUEuropean 120IG 0.367 0.533 0.100 0.254 0.633 0.367
HapMap-HCBAsian 90IG 0.333 0.556 0.111 0.273 0.611 0.389
HapMap-JPTAsian 88IG 0.409 0.386 0.205 0.200 0.602 0.398
HapMap-YRISub-Saharan African 120IG 0.833 0.150 0.017 0.479 0.908 0.092
AGI_ASP populationmultiple 76IG 0.658 0.289 0.053 0.655 0.803 0.197
ss4919910JBIC-allele 1476AF 0.690 0.310
ss68960976HapMap-CEUEuropean 120GF 0.367 0.533 0.100 0.633 0.367
HapMap-HCBAsian 90GF 0.333 0.556 0.111 0.611 0.389
HapMap-JPTAsian 90GF 0.422 0.378 0.200 0.611 0.389
HapMap-YRISub-Saharan African 120GF 0.817 0.167 0.017 0.900 0.100
Concordant GenotypeTotal SampleA/AA/GG/G
ss243760247139238
ss48415801308
ss6896097626914410025
RefSNP Genotype SummaryTotal IndividualA/AA/GG/G
rs96103037118011931
Discordant Genotypes:
Indiviudal
SampleID
SubSNP(ss)GenotypePopulation
Handle
Submitter
Population
Submitter
SampleID
SampleID
Alias
Submission
Batch
NCBI
ProbeID
5237ss48415801T/TCSHL-HAPMAPHapMap-YRINA18501YOR004.03r23_ch5_YRI_imsut-riken:genotyping
5237ss68960976A/GCSHL-HAPMAPHapMap-YRINA18501YOR004.03chr5-HapMap-YRI
Genotype data submitted for380 samples from371 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .