Reference SNP(refSNP) Cluster Report: rs732889

Reference SNP(refSNP) Cluster Report: rs732889

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:	T
Clinical Association:	unknown

HGVS Names
NM_052896.3:c.3932+3029G>C
NT_032977.8:g.4127419G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5157213 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs732889 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss78574	TSC-CSHL\|TSC0022461	fwd/B	C/T	actgtttgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	09/06/00	10/25/06	86	Genomic	95 %
ss5157213	TSC-CSHL\|TSC0247049	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	09/19/02	10/25/06	108	Genomic	unknown
ss5461245	TSC-CSHL\|TSC0180544	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	09/21/02	10/10/03	108	Genomic	unknown
ss14424865	WUGSC_SSAHASNP\|chr1.NT_004511.16_4093903	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	11/05/03	11/22/03	119	Genomic	unknown
ss16392997	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_004511.16_4093903	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	02/17/04	03/04/04	120	Genomic	unknown
ss17330395	CSHL-HAPMAP\|CSHL-HuCC-200402.chr1.NT_004511.16_4093903	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	02/19/04	03/04/04	120	Genomic	unknown
ss20512494	SSAHASNP\|WGSA-200403-chr1.chr1.NT_004511.16_4093903	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	03/18/04	03/18/04	121	Genomic	unknown
ss43964795	ABI\|hCV3138304	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	07/18/05	11/03/06	126	Genomic	unknown
ss66163032	AFFY\|SNP_A-2171006	fwd/B	C/T	caatacaccaagtacc	gcgtacctaccgccta	10/27/06	08/14/07	127	Genomic	unknown
ss66594102	ILLUMINA\|HumanHap300v1.1_rs732889	fwd/T	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	11/09/06	11/09/06	127	Genomic	unknown
ss67570436	ILLUMINA\|HumanHap550v1.1_rs732889	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	11/14/06	11/14/06	127	Genomic	unknown
ss67950586	ILLUMINA\|HumanHap650Yv1.0_rs732889	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	11/14/06	11/15/06	127	Genomic	unknown
ss68763049	PERLEGEN\|PGP10900754	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	01/30/07	08/14/07	127	Genomic	unknown
ss70923770	ILLUMINA\|HumanHap550v3.0__rs732889	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacacacagt	04/20/07	03/31/08	130	Genomic	unknown
ss71524255	ILLUMINA\|HumanHap650Yv3.0_rs732889	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	04/23/07	04/23/07	127	Genomic	unknown
ss74958652	ILLUMINA\|ILMN_Human_1M_rs732889	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	08/28/07	08/29/07	129	Genomic	unknown
ss76207733	AFFY\|AFFY_6_1M_SNP_A-2171006	fwd/B	C/T	caatacaccaagtacc	gcgtacctaccgccta	08/28/07	08/30/07	130	Genomic	unknown
ss78606479	HGSV\|Cor12878_SNV_20070510.chr1_33824594	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	10/17/07	10/20/07	129	Genomic	unknown
ss79254454	ILLUMINA\|HumanHap300v2.0_rs732889	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	04/18/07	11/18/07	130	Genomic	unknown
ss83539023	KRIBB_YJKIM\|KHS485132	fwd/B	C/T	actgtgtgtgacaacaatacaccaagtacc	gcgtacctaccgcctacacccaaatggcgt	12/04/07	12/05/07	130	Genomic	unknown
ss83874915	HGSV\|Cor18555_SNV_20070510.chr1_33824594	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	11/27/07	12/06/07	130	Genomic	unknown
ss85748946	HGSV\|Cor19129_SNV_20070510.chr1_33824594	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	12/06/07	12/10/07	130	Genomic	unknown
ss85948301	HGSV\|Cor18517_SNV_20070510.chr1_33824594	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	12/06/07	12/10/07	130	Genomic	unknown
ss85956107	HGSV\|Cor18956_SNV_20070510.chr1_33824594	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	11/30/07	12/10/07	130	Genomic	unknown
ss87345479	BCMHGSC_JDW\|JWB-0031635	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	02/26/08	02/26/08	129	Genomic	unknown
ss99199012	HUMANGENOME_JCVI\|1103675064204	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	04/03/08	04/03/08	130	Genomic	unknown
ss110272716	1000GENOMES\|NA19240_2008_12_16_40949_chr1_33928088	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	12/16/08	12/17/08	130	Genomic	unknown
ss118610389	ILLUMINA-UK\|NA18507_000040297_NCBI36.1_chr1_33928088	rev/T	A/G	acgccatttgggtgtaggcggtaggtacgc	ggtacttggtgtattgttgtcacaaacagt	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 TCTGTTTGTT TACTACCTGG TTGTGCCTGT GCCAGATGCT GGCATTATAT AAATGAATGA
 GATGTGGCCA TGGTTCACAA AGAGCAGACG CACATGTCTG TCCAGAACAA GGTGGTGGCA
 CAATGAGGAA GGGGAATGAA AAAGCAGGAC AGGAggagat gggagaagtt attctggaaa
 aggtgaccct agagctgagt cctgaaggaa ggagaggagg ttgccaggta gccaaggagg
 aaggTGGGTG GGAGGGTAAT GGGCCTCTAG GCAGAGTGAA GCAGTGTGGT CAGCCTCAAG
 GAGCTGGAAA TGGTTCCCGC AGCTGGATGA TCACCTGCGA TTTGGTGGGT GGCGGCATTC
 ATGGGAGATG AAGCTGGTGG TGGAGGCTGT GGGGAGCACA GAGGGCGTTG GGGCTATGAG
 GCTGCGTTTT GACAGCTCCT GGCAGTTTGG AGGAGAATGG GCGGAGTGGG ACGGGCTGGG
 CCGGTAAGCG CAGTGAGGAA GCTGCCTCCA GAGTGTGGCT GGGGACGAGG AGGCCAGAAG
 TCAGGCAGTG GCAGTGGAGA TGGAGAAGAA GAGAAAATTC AGGGGACATT CAAGTGATCA
 CACCAACTTT TCTCAACTAC TGTGTGTGAC AACAATACAC CAAGTACC
 Y
 GCGTACCTAC CGCCTACACC CAAATGGCGT TACTATTTTG CCATATATGC TTATGTGCTC
 TCTTTGTGCT TCTCTTTCCA TCCTTTTGTT TTCCTTTTTG CTGAGCTGCT GGAAAGTACA
 CTGTCAACAT CATGATACTT CATTTCTAGA TGCTTTGGCA CACATCGTCT AAAGAGAAGG
 ATGTGTTCAT CCATGGCATA GCGGCCGTAA TGTACCTAAA AGGCACAGCA TTAATTCTCT
 GGGAATTAAG GAGAGCAGAG CAGATCTAGG TGTGGCTGGC ACAAGGAAAT TACAATAAAC
 TGATGAATGG ATTTCTGGGC AGTAGTGAGG ACCATTTTCA CTGATGAGAA TGGTGGCTAT
 GGGGGTGGAG GGGAGACAGG AGGCGCCTTT CTAGCCCTCA GGAAGACAAG ATCAAAACCA
 ATACAGGAAA CGTCCTCTCC AGAGTAACAT AGCAAGAAAT ATGAAGTCAT GGGGGGCATG
 CTGAGGATCC CAAAATGGGA AGAAGAAAGT AAAGGTCCAA AGAAGGTAAA GATAACATCA
 GTCCTTAGTC TGGATGGCTT CTTGGAGCCA CAGCAACCTC AAAGGAGCTA ATGTGAAGTA
 AGAAGATGTC TTCCCAGTTT CACTGAGAGC TGCAGAAAGA TGGAGATAGA GTGGCAAGAC
 ACTGTCCCTT CCTCATTCTC CCACCCCAGT CTGCCA

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

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
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

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

Resource

Submitter-Referenced
GenBank
NT_004511 ABBA01023373 AC025303.1 AL139140.4 AL161623.10 AL161643.3

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss43964795	AoD_African_American		90	AF					0.330	0.670

	AoD_Caucasian		92	AF					0.420	0.580

ss5157213	HapMap-CEU	European	116	IG	0.172	0.483	0.345	1.000	0.414	0.586

	HapMap-HCB	Asian	90	IG	0.133	0.533	0.333	0.479	0.400	0.600

	HapMap-JPT	Asian	88	IG	0.068	0.409	0.523	1.000	0.273	0.727

	HapMap-YRI	Sub-Saharan African	120	IG	0.167	0.400	0.433	0.294	0.367	0.633

ss66163032	HapMap-CEU	European	118	GF	0.169	0.458	0.373		0.398	0.602

	HapMap-HCB	Asian	90	GF	0.111	0.556	0.333		0.389	0.611

	HapMap-JPT	Asian	90	GF	0.067	0.400	0.533		0.267	0.733

	HapMap-YRI	Sub-Saharan African	120	GF	0.167	0.400	0.433		0.367	0.633

ss68763049	HapMap-CEU	European	120	GF	0.167	0.467	0.367		0.400	0.600

	HapMap-HCB	Asian	90	GF	0.133	0.533	0.333		0.400	0.600

	HapMap-JPT	Asian	90	GF	0.067	0.400	0.533		0.267	0.733

	HapMap-YRI	Sub-Saharan African	120	GF	0.167	0.400	0.433		0.367	0.633

ss76207733	ICMHP		10	IG	0.200	0.400	0.400		0.400	0.600

ss78574	TSC_42_AA		82	AF					0.366	0.634

	TSC_42_C		82	AF					0.341	0.659

	TSC_42_A		82	AF					0.317	0.683

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss5157213	1206	205	516	449
ss66163032	268	35	126	107
ss68763049	269
ss76207733	5	1	2	2
ss99199012	1

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs732889	1213	208	530	459

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5185	ss5157213	C/C	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	r27_ch1_CHB_illumina:human_1m_beadchip	236256
5185	ss66163032	C/T	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	chr1-HapMap-HCB
5185	ss68763049	G/G	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	chr1-HapMap-HCB

Genotype data submitted for	1213	samples from	1213	individuals	Individual with multiple genotypes submission:	270

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .