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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs730907          
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:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NT_034772.5:g.20473644A>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 ss76076 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs730907 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
ss76076TSC-CSHL|TSC0018534byFreqfwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag09/06/0004/07/0486Genomic95 %
ss10260450BCM_SSAHASNP|chr5.NT_034772.4_20473652rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa06/27/0310/10/03116Genomicunknown
ss11761325WI_SSAHASNP|chr5.NT_034772.4_20473652rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa07/04/0310/10/03116Genomicunknown
ss14672548WI_SSAHASNP|chr5.NT_034772.5_20473644rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa11/05/0311/22/03119Genomicunknown
ss20249731CSHL-HAPMAP|CSHL-HuFF-200402.chr5.NT_034772.5_20473644rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa02/21/0403/04/04120Genomicunknown
ss22263430SSAHASNP|WGSA-200403-chr5.chr5.NT_034772.5_20473644rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa03/21/0403/21/04121Genomicunknown
ss23922094PERLEGEN|afd3596867byFreqrev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa08/10/0409/13/04123Genomicunknown
ss44595291ABI|hCV1990994byFreqrev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa07/19/0511/03/06126Genomicunknown
ss66723276ILLUMINA|HumanHap300v1.1_rs730907fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag11/09/0611/09/06127Genomicunknown
ss67567725ILLUMINA|HumanHap550v1.1_rs730907fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag11/14/0611/14/06127Genomicunknown
ss67947064ILLUMINA|HumanHap650Yv1.0_rs730907fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag11/14/0611/15/06127Genomicunknown
ss68947325PERLEGEN|PGP03596867byFreqrev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa01/30/0708/14/07127Genomicunknown
ss70922338ILLUMINA|HumanHap550v3.0__rs730907fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag04/20/0703/31/08130Genomicunknown
ss71522472ILLUMINA|HumanHap650Yv3.0_rs730907fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag04/23/0704/23/07127Genomicunknown
ss75652679ILLUMINA|ILMN_Human_1M_rs730907fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag08/28/0708/29/07129Genomicunknown
ss76842956AFFY|AFFY_6_1M_SNP_A-8704534fwd/BC/Tgagtgaaaggctgctcctactcctttacatgt08/28/0708/30/07129Genomicunknown
ss77695955HGSV|Cor12156_SNV_20070510.chr5_118086530rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa10/09/0710/14/07129Genomicunknown
ss78595652HGSV|Cor12878_SNV_20070510.chr5_118086530rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa10/17/0710/20/07129Genomicunknown
ss79253648ILLUMINA|HumanHap300v2.0_rs730907fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag04/18/0711/18/07130Genomicunknown
ss83537857KRIBB_YJKIM|KHS484880fwd/BC/Tttctcccatttttagagtgaaaggctgctcctactcctttacatgtatccaccttgggag12/04/0712/05/07130Genomicunknown
ss84696397HGSV|Cor19240_SNV_20070510.chr5_118086530rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa11/30/0712/07/07130Genomicunknown
ss93226859BCMHGSC_JDW|JWB-2029959rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa02/26/0803/04/08129Genomicunknown
ss98643118HUMANGENOME_JCVI|1103654204204rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa04/01/0804/01/08130Genomicunknown
ss1093562881000GENOMES|CEU.trio.12.15.2008_1347809_chr5_118086530rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa12/15/0812/16/08130Genomicunknown
ss1131442331000GENOMES|NA19240_2008_12_16_1209461_chr5_118086530rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa12/18/0812/18/08130Genomicunknown
ss116780987ILLUMINA-UK|NA18507_000148740_NCBI36.1_chr5_118086530rev/TA/Gctcccaaggtggatacatgtaaaggagtaggagcagcctttcactctaaaaatgggagaa01/17/0901/18/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs730907|allelePos=245|totalLen=648|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TGCTCAGGTC AGATGTTAGT GAGGTCAATA AAAATAACAA GAAAAATGAA ACACTTAAAG
 GGTCATTGAA CTTCTCAAAA TGAAACTGTT ATGTAATCAC AGATTCTATT TTATGGCTCT
 CATTGGGCTG GAAATGATTC AATGTATGCC CATACAATTA AAACTATCAG ACAACCTGGG
 AGAATTGGAC AGAGCCTTTT GGATAGAGGC TGTTTTCTCC CATTTTTAGA GTGAAAGGCT
 GCTC
 Y
 CTACTCCTTT ACATGTATCC ACCTTGGGAG ACTTATTTCT TTTACTTATG GTCATCTCTT
 GTGTCCTTCA AAAGGTACAA ACAAGGTTAC CAAAGTCAAA TATCGACAGA GGACAATGGG
 TAACTTGAGT GAGCAGGGTT ATCTGAACAG TGGCTGCAGT TGACTACAGA AGGTTGCCAC
 ACCCAAAACT GGCAGTGAAT CCTCTCATCC AGCAGACCAA TGGCCCTTAG TAATGCAGGC
 CCTGTGTTGT CATATCTTCT GCTTTTTACT CAAATCAGAA GTTGACTTTT ACATTTTGTG
 TGTGTGTGCA CGTGCGCTCA GACCAACCGG AACATATCTG TAATCTCTGT GGGCCAGGGT
 TGCTGGTGTG CAACTTCTGG ATTTTGCTTT TCTTCAGACT GTA

  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
NT_034772 ABBA01068989
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss23922094 AFD_EUR_PANEL European 48 IG 0.375 0.583 0.042 0.150 0.667 0.333
AFD_AFR_PANEL African American 46 IG 0.565 0.348 0.087 0.655 0.739 0.261
AFD_CHN_PANEL Asian 48 IG 0.333 0.500 0.167 1.000 0.583 0.417
ss44595291 AoD_African_American 90 AF 0.800 0.200
AoD_Caucasian 92 AF 0.670 0.330
AoD_Chinese 90 AF 0.530 0.470
AoD_Japanese 90 AF 0.530 0.470
ss68947325 HapMap-CEU European 120 GF 0.617 0.300 0.083 0.767 0.233
HapMap-HCB Asian 90 GF 0.289 0.511 0.200 0.544 0.456
HapMap-JPT Asian 90 GF 0.267 0.467 0.267 0.500 0.500
HapMap-YRI Sub-Saharan African 120 GF 0.700 0.267 0.033 0.833 0.167
ss76076 TSC_42_AA 84 AF 0.750 0.250
TSC_42_C 82 AF 0.683 0.317
TSC_42_A 70 AF 0.557 0.443
HapMap-CEU European 120 IG 0.617 0.300 0.083 0.251 0.767 0.233
HapMap-HCB Asian 90 IG 0.267 0.533 0.200 0.584 0.533 0.467
HapMap-JPT Asian 90 IG 0.267 0.467 0.267 1.000 0.500 0.500
HapMap-YRI Sub-Saharan African 118 IG 0.695 0.271 0.034 1.000 0.831 0.169
CHMJ Asian 74 IG 0.500 0.500
Concordant Genotype Total Sample C/C C/T T/T
ss23922094 71
ss68947325 269
ss76076 1206 631 453 99
ss98643118 1
RefSNP Genotype Summary Total Individual C/C C/T T/T
rs730907 1264 631 453 99
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5167 ss76076 C/T CSHL-HAPMAP HapMap-HCB NA18611 CH18611 r27_ch5_CHB_illumina:human_1m_beadchip
5167 ss68947325 G/G CSHL-HAPMAP HapMap-HCB NA18611 CH18611 chr5-HapMap-HCB
Genotype data submitted for1279 samples from1264 individualsIndividual with multiple genotypes submission:276

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .