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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs949835          
refSNP ID: rs949835
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:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_000547.3:c.180-4434A>G
NM_175719.1:c.180-4434A>G
NM_175721.1:c.180-4434A>G
NM_175722.1:c.180-4434A>G
NT_022221.12:g.156712A>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 ss5190688 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs949835 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
ss1393038TSC-CSHL|TSC0008551fwd/BC/Ttcggctgacatgtttgtaaaaggtactataagtcatgaactttgaggacactgagattat09/06/0010/10/0386Genomic95 %
ss5190688TSC-CSHL|TSC1098787byFreqfwd/BC/Ttcggctgacatgtttgtaaaaggtactataagtcatgaactttgaggacactgagattat09/20/0210/25/06108Genomicunknown
ss17638990CSHL-HAPMAP|CSHL-HuCC-200402.chr2.NT_033000.6_156712rev/TA/Gataatctcagtgtcctcaaagttcatgacttatagtaccttttacaaacatgtcagccga02/19/0403/04/04120Genomicunknown
ss44217143ABI|hCV8760422rev/TA/Gataatctcagtgtcctcaaagttcatgacttatagtaccttttacaaacatgtcagccga07/18/0507/18/05126Genomicunknown
ss91028087BCMHGSC_JDW|JWB-1189794rev/TA/Gataatctcagtgtcctcaaagttcatgacttatagtaccttttacaaacatgtcagccga02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs949835|allelePos=429|totalLen=1377|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTTCtgtgtt aggccatttt cacattgcta taaagaaata cctgagactt ggtaatttac
 ccagaaaaga agtttaattg gctcacggtt cttctggcta tataagcatg gctcctgcac
 ctgcctggct tctggtgagg gcctcatgaa gccgacaacc atggcagaag ttgaatgggg
 agtggtcagg tcccggagta agagcaggag caggagagta gagtggggga gatgccacag
 acttttaaac aaccagatct cacgtgaagt aactgagcaa aaactccctt atcaccaacg
 ggatggggca aatcactcaC CATATATATT AGAAATAACT TCATGTACAT ACAAATGCGT
 ATGACATTTA ACTTAAAATA TAAAACACGT GTTTTATATC GGCTGACATG TTTGTAAAAG
 GTACTATA
 Y
 Agtcatgaac tttgaggaca ctgagattat agctacttac aactaacaca ttagccagcc
 atagttcatg gatgccagcc aaagacagga gactctcggc ccagacacaa gtgacattgt
 cagtcacagc agcagcagag ccagagtgta agcacctgtg caggttcccc AGGACTCGCC
 ATGGTAGACA GGATAGCAAC CCTCCCCAAA ACGCGTGCTT TCCTTGGAGA CATTTATCTA
 AAATCTATCT GAGCAAGACA TTTGGCTAAT AGGAAGAACA AGAATTCTCT GGAGATCTGA
 AGGCCAAGGG TGCTCCTTTT GATGAAATCC ACTTTCTCTG CTTCCTAGAA CATCACCTGC
 ACCCACTCGA GGGCTCACCT GTCTCATCCC TTCTTTTGCC TGGCACCCAT GGGACAACAC
 AATCTGGGCC CAAAAGGGGT ACGTCAGGAA AGCAGGGGTC TGGGAAACTG AGCTCAGCTC
 TTGACAGTGA CGTGGAGGGT ATCACCCAGT GGATCCCCCG GATAGGTCCC CAGGCCATGC
 TGCCCATGCC AGCCCTTCCT GTCCCTGCAA CTGCCGTGTA GCTCAGAGGA CTCTCCCTTG
 CTGGCTGGTC ACTTTCCCGT CATGTCCATG TTCTGCAGAG CCCAGCCTGT GGGGAGCTCA
 GTTCAGGAGA GCCTGGAAAG GTGCTTCAAC CACCCCACAA GCCACAGTCT GCTCTGTTCA
 TCTGCTGCTA TTTCCCAGGG GCCCCAGCCA TGGGTCATTC CGAATGCAGA CAGTTTGCAG
 CCCAGCCCAG GGCTGCATGT TACTTTAAGA CCTCAGCTTC AGAACATAAG CAAGGTATTA
 ATAGGTGACA CTTTCAGGCT CTTAATTGCA GCAAAATATC TGAAAATCAA ACTCAAATTA
 GGGAAACTTT GACTCTAGCT GGTTTCGCAT TCTTAATGTG AAGAGCCC

  GeneView back to top
GeneView via analysis of contig annotation: TPO thyroid peroxidase
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_022221->NM_000547
function
referenceNT_022221->NM_175719
function
referenceNT_022221->NM_175721
function
referenceNT_022221->NM_175722
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_022221->NM_000547->NP_000538156712forwardintron
referenceNT_022221->NM_175719->NP_783650156712forwardintron
referenceNT_022221->NM_175721->NP_783652156712forwardintron
referenceNT_022221->NM_175722->NP_783653156712forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs949835 maps exactly once on NCBI human chromosome 2
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
2NT_022221.121567121411783minusAref_assemblyreferencereferenceview428
2NW_001838759.11457171424103minusAalt_assembly_8HuRefHuRefview428
2NW_927719.114141671482232minusGalt_assembly_1CeleraCeleraview428

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_033000
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
ss5190688HapMap-CEUEuropean 120IG 0.083 0.317 0.600 0.294 0.242 0.758
HapMap-HCBAsian 90IG 0.022 0.244 0.733 1.000 0.144 0.856
HapMap-JPTAsian 88IG 0.023 0.182 0.795 0.527 0.114 0.886
HapMap-YRISub-Saharan African 120IG 0.167 0.550 0.283 0.403 0.442 0.558

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.376+/-0.21627021000

  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, NCBI
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .