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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs219803          
refSNP ID: rs219803
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:T
Clinical Association:unknown
HGVS Names
NM_003496.1:c.9314+855T>C
NT_007933.14:g.23817798T>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 ss1724255 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs219803 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
ss285919KWOK|OVLP-000621-245378rev/TA/Gcagatacagggtttacttgggggatgatggaatattctagaattagctagtggtaatggt06/30/0010/10/0379Genomic97 %
ss1204754KWOK|OVLP-000804-58939fwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg09/02/0010/10/0386Genomic97 %
ss1724255KWOK|OVLP-000925-185037byFreqfwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg10/05/0010/25/0687Genomic97 %
ss2435155SC_JCM|AC004893.1_27307fwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg11/03/0010/10/0392Genomicunknown
ss14537997WUGSC_SSAHASNP|chr7.NT_007933.13_23817106fwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg11/05/0311/22/03120Genomicunknown
ss23762402PERLEGEN|afd4083646byFreqfwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg08/10/0409/13/04123Genomicunknown
ss42932455ABI|hCV2270567fwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg07/18/0507/18/05126Genomicunknown
ss84000548HGSV|Cor19240_SNV_20070510.chr7_98228173fwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg11/30/0712/06/07130Genomicunknown
ss85500918HGSV|Cor19129_SNV_20070510.chr7_98228173fwd/BC/Taccattaccactagctaattctagaatattccatcatcccccaagtaaaccctgtatctg12/06/0712/09/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs219803|allelePos=304|totalLen=3292|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GAGAAGTAAA CGTCAGAGGA GATTTTGTAA ATATCATGCA AATGAGGTAG ACTCACAAGA
 TGCTGCCTGT TGCCTTGTGT AGGCTCCAGT GCCTGCTTTT CACATCTTCA GTCTGTGGGG
 CTTGCATGTT TAGCTTATTT TTAAATTAGG AAGCAGTTTT GTCAACATAA AAAGGTTTTA
 TCTTTTTGTG TAATGTTTTA aattcatgtg acagacacaa ccattccaaa gtgtacaatt
 tagtgggttt tagtatattt acagtgttac acaaccatta ccactagcta attctagaat
 att
 Y
 ccatcatccc ccaagtaaac cctgtatctg ttagtagtca ctctcctttc tcccctcccc
 ctttctcttg acaactacta atgtactttc tgcctctatg gatttgctta ttctgaacat
 tcatataaat agaagcatac actgtgtggc cttttgtgac tgtcttcttt cacttagcag
 gatgttttca agcttcatcc atgtgctgtc atgtatcagt aacctgttct ttttcatggc
 tgaataatat tccattggat atccatacat tttgtttatc catgcagcag ttgatggatg
 tgtgggttgt tcctactttt tagctacatg agtaatgctg gtgtaaacac tgaatatgtg
 tctttgtgtg agcatgtttg agttctcttg gttatatacc tggggacaga atatctgggt
 catattgtac ttctctgttt atctttttga gacattgtca atcttccaca gttggccgta
 ccatttttac attcccacca gcaatgttta aggttttaat ttctccatat cctcaccagc
 acttgttatt ttcttattat ttatctgatt atagccatcc taatgagtat aaaatatatt
 tcattgtggt tttgaattgc attttcctaa tgactgttga tgctgagctt cttttcttgg
 ttttgattgt tagtttgtaa ttctttatag gtctggataa aagtctcttg cagatatatg
 atttccaagt attttgtcac gttctgtggg ctgtcttttc acttttttga tagtgtcctt
 taatgtacaa gtttttaatt ttgatgaagt ccaattcatg tatttttttc ttttgttgct
 catacttttc acgtcttcta agaaaccata ccctaatcca ggatcagaag catttattct
 tatgttttct tctaagcatt tcatagattt agctcttaca tttgggtctc tgatccattt
 tgaataattt tttatgtggt gtgaggtagg ggtctatatt tattatgctg catgtggata
 tacggttgtc ccagcaccat ttgctgaaaa gtctagtctt tctccattga atggtcttga
 caccctcatc aaaaatcagt tgaggccagg cccagtggct cacacctgta atcctagcac
 tttgggaggc tgaggtggga ggatcacttg agcccaggag tttgagacca acctggacaa
 tatagtggag acccccattt ccaaaaccca aaaaacaaaa atccgttgac cattttttgt
 gggcttattt ctggactctc acttctattc cattgatctg ctatgtAGAG TCTCATattt
 ccatatgaat tttaggttat tttcatgtat ttctgccaaa acagttggaa ttacgacaga
 gattgcattg aatctgtaga tcagtttgtg agcattttgc catctgaagc aagttttcca
 gtttgtgaac acgagatgtc tttccactag tttaggtctt ctttagttta attcaacaat
 gttttttagt ttttagtgta caagtcttgc acttatgtta aatttattcc tcaatattgt
 cacgtgaatg gagccatttt cttcattttc acattgctca ttgctaacat ttggaaatac
 cagggttttg tatattgatc ttagatttct caaccttgct gagtgtattt gctctaatag
 ctttttgggg attcttcttt tctgtgtata agatcgtgtc aactgcaggt agagatggac
 tgacatcttc tcttccaata aggatgcctt ttatttcttt ttcttcccaa ttgccctgac
 tagaacctca agtacagtgc tgaattaaag agatgagatc cttgtctttt tcttgatctt
 ggggaaagcc attcagtctt tcagccttga gtatgatgtt agctgtgggt gttctgtaga
 tgccttttat aagcttgagg aacttccctt ctgttctaaa tttgctgggt atttttatca
 tgagatgttg ttggactttt ttcaaatggc tttttctgtg tcctctgaga tgattgtgtt
 ttttttcctt cattgtttta atgtggtata tcacattgat tggttttatt tatattgact
 tttttgtttt ctgtgttgaa ccacccttat tgctgggata aatcccactt ggtcatgatg
 gataatcctt ttaatccgct gctggagttg ggttgctcat ttttgtcgag gatgtttgcg
 tctgtatcat aaagcacctg ggtctgaagt tcccttGCTA TGTCTGGtac attgctggtg
 taatagtgaa gcggtataac tgctgtggaa acagtttgac ggttccacaa aaagtaagca
 tagagttccc acgtgaccag catttccact ccctggtata cacccagaag tgttgaaaca
 aacagatacc tgttcgggaa tgtttgtagc aggactattt gcaataatca agatgtggaa
 acaacacaaa tgaacagata aacaaaatgt ttatgttcta tgtgtgcaat ggaatgttat
 tcacttgtta aagagaatga agcactgaca caggcttcaa catggataaa cctcgaaaac
 actgtgctag gtgaaagaag ccagattcaa aagatcacat ggtgtatgat tcaatttata
 tgaaatgtac agaaccggtc aatccacaga gacagaaggc agactgcagg ttcccagggg
 ctggaggtgg gaggggttca gagcgactgc ttatggggcg gttgcacaac attgtgaatg
 gaccaaatgc cccgcagtgt tcattttata atggttaatt tcagattacg tgaagctcgc
 ttcaattgaa aaCCATACAC GTTTTGGTTT TCTGTCTCCT CACAGGTCCG AGGAGGCAAA
 CAAAGCCTTC TCTGCAGCTG TGCAGATGCA CGATGTGCTG GTGAAAGCCT GGGCCATGTG
 GGGCGACTAC CTGGAGAACA TCTTTGTGAA GGAGCGGCAG CTGCACCT

  GeneView back to top
GeneView via analysis of contig annotation: TRRAP transformation/transcription domain-associated protein
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_007933->NM_003496
svfunction
HuRefNW_001839064->NM_003496
svfunction
CeleraNW_923574->NM_003496
svfunction
CRA_TCAGchr7v2NT_079595->NM_003496
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_007933->NM_003496->NP_00348723817798forwardintron
HuRefNW_001839064->NM_003496->NP_003487236312reverseintron
CeleraNW_923574->NM_003496->NP_00348721851413forwardintron
CRA_TCAGchr7v2NT_079595->NM_003496->NP_00348723840755forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs219803 maps exactly once on NCBI human chromosome 7
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
7NW_001839064.223631293216398minusAalt_assembly_8HuRefHuRefview303
7NW_923574.12185141393312376plusTalt_assembly_1CeleraCeleraview303
7NT_079595.22384075597939543plusTalt_assembly_2CRA_TCAGchr7v2CRA_TCAGchr7v2view303
7NT_007933.142381779898421458plusTref_assemblyreferencereferenceview303

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_007933 AC061971 AC061971.2
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC004893.1 NC_000007.12 AC099650.3

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1724255HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 118IG 0.390 0.458 0.153 1.000 0.619 0.381
ss23762402AFD_EUR_PANELEuropean 48IG 1.000 1.000
AFD_AFR_PANELAfrican American 46IG 0.348 0.435 0.217 0.584 0.565 0.435
AFD_CHN_PANELAsian 48IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.292+/-0.24633226090

  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 .