Reference SNP(refSNP) Cluster Report: rs729421

Reference SNP(refSNP) Cluster Report: rs729421

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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NG_007150.1:g.412A>G
NM_004581.3:c.-255C>A
NM_004581.3:c.1258A>G
NM_182836.1:c.1258A>G
NM_182836.1:c.3G>A
NP_004572.3:p.Thr420Ala
NP_878256.1:p.Thr420Ala
NT_026437.11:g.5736801T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss74175 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs729421 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
ss74175	TSC-CSHL\|TSC0031655	fwd/T	A/G	ccactccaggccgtggaccccatgcgggca	cgtatctggatgacctgcgcagcaagttct	09/06/00	04/07/04	86	Genomic	95 %
ss3239017	YUSUKE\|IMS-JST049102	fwd/T	A/G	ccactccaggccgtggaccccatgcgggca	cgtatctggatgacctgcgcagcaagttct	09/05/01	10/10/03	100	Genomic	unknown
ss5987005	SC_JCM\|NT_025892.9_5059401	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	01/10/03	10/10/03	111	Genomic	unknown
ss10749574	BCM_SSAHASNP\|chr14.NT_026437.10_4657089	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	06/30/03	10/10/03	116	Genomic	unknown
ss16239659	CGAP-GAI\|1476341	fwd/T	A/G	accctcaaggccgtggaccccatgcgggca	cgtatctggatgacctgcgcagcaagttct	11/18/03	11/22/03	120	cDNA	unknown
ss16658046	CSHL-HAPMAP\|CSHL-HuAA-200402.chr14.NT_026437.10_4657089	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	02/17/04	03/04/04	120	Genomic	unknown
ss23799214	PERLEGEN\|afd0155060	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	08/10/04	09/13/04	123	Genomic	unknown
ss43589184	ABI\|hCV1258505	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	07/18/05	11/03/06	126	Genomic	unknown
ss48403838	APPLERA_GI\|hCV1258505	fwd/T	A/G	ccactccaggccgtggaccccatgcgggca	cgtatctggatgacctgcgcagcaagttct	09/28/05	11/03/06	126	Genomic	unknown
ss65729326	ILLUMINA\|Human1-rs729421	fwd/T	A/G	ccactccaggccgtggaccccatgcgggca	cgtatctggatgacctgcgcagcaagttct	10/10/06	10/10/06	127	Genomic	unknown
ss69151253	PERLEGEN\|PGP00155060	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	01/30/07	08/14/07	127	Genomic	unknown
ss74903450	ILLUMINA\|ILMN_Human_1M_rs729421	fwd/T	A/G	ccactccaggccgtggaccccatgcgggca	cgtatctggatgacctgcgcagcaagttct	08/28/07	08/29/07	129	Genomic	unknown
ss79007721	HGSV\|Cor18507_SNV_20070510.chr14_23806801	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	10/19/07	10/21/07	129	Genomic	unknown
ss85468770	HGSV\|Cor19129_SNV_20070510.chr14_23806801	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	12/06/07	12/09/07	130	Genomic	unknown
ss115411746	1000GENOMES\|NA19240_2008_12_16_2696066_chr14_23806801	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	12/18/08	12/19/08	130	Genomic	unknown
ss118380706	ILLUMINA-UK\|NA18507_000007408_NCBI36.1_chr14_23806801	rev/B	C/T	agaacttgctgcgcaggtcatccagatacg	tgcccgcatggggtccacggcctggagtgg	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 ACATGCATAC CCTGCCCACC TCATCCACTC CAGGCCGTGG ACCCCATGCG GGCA
 R
 CGTATCTGGA TGACCTGCGC AGCAAGTTCT TGCTGGAGAA TAGCGTGCTC AAGATGGAGT
 ATGCCGAGGT GCGTGTGCTG CACCTGGCTC ACAAGGTATG GGCTGCCATG CATGCCTTCC
 CCTGGCCCTC ATCCCGCTGG CCTCCCCACG TCCCTGACTT TGCCCCCAGT CTCAGGTGCC
 TTTGTGGACT TCCAATCAAG ATAGAGTTCA TCCCTGCCTC CCAGCTTGCT CCTCTTCCAG
 GCCTTTCTGT CACTCAGCCC ATTCTTCTTC TTGCCACTCA CTTTCAAATC CCGAGTCACC
 AGGACCTCCT TGTGCTGTTT CTTCCCCAGG CTGGTCACAG CTTCATCTTC CTTCAGAGTG
 ACCGCTAGCC CACTCCTCCC ACACATTCCA GCACATCTCA CCCTGGAGCA ACCTCCAATA
 CCTGAAGGCC AAATACTTTC CAGAGATTCC TGAGAAGTTG TCCAGGCTCC ACTTTCCTAG
 TCCTTCCCAA CACATTAGTT TTATCACATC ACCACAGCCC ACCTCCATTC CTGCCAAACT
 CATCTCTGCC TCATCAGGAC CAGTCCCCAT GGGGGACCAG TCTTTGTTTA CCCAGCACCC
 TCCACTGGCC CCTGTACCTT CGAACTCCAG GCCTTCTCCT TCTTACCACC CC

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_026437 AA134051

dbSNP Blast Analysis

UniGene Cluster ID
377992

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23799214	AFD_EUR_PANEL	European	48	IG	0.583	0.333	0.083	0.655	0.750	0.250

	AFD_AFR_PANEL	African American	46	IG	0.130	0.391	0.478	0.655	0.326	0.674

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.500	0.458	0.317	0.292	0.708

ss3239017	JBIC-allele		1498	AF					0.397	0.603

ss43589184	AoD_African_American		90	AF					0.270	0.730

	AoD_Caucasian		92	AF					0.600	0.400

	AoD_Chinese		90	AF					0.290	0.710

	AoD_Japanese		90	AF					0.410	0.590

ss48403838	AGI_ASP population	multiple	60	IG	0.333	0.333	0.333	0.100	0.500	0.500

ss69151253	HapMap-CEU	European	120	GF	0.433	0.450	0.117		0.658	0.342

	HapMap-HCB	Asian	90	GF	0.111	0.533	0.356		0.378	0.622

	HapMap-JPT	Asian	90	GF	0.267	0.378	0.356		0.456	0.544

	HapMap-YRI	Sub-Saharan African	120	GF	0.083	0.183	0.733		0.175	0.825

ss74175	TSC_42_AA		84	AF					0.310	0.690

	TSC_42_C		82	AF					0.598	0.402

	CEPH		91	AF					0.909	0.091

	HapMap-CEU	European	116	IG	0.414	0.466	0.121		0.647	0.353

	HapMap-HCB	Asian	90	IG	0.111	0.533	0.356	0.371	0.378	0.622

	HapMap-JPT	Asian	88	IG	0.273	0.364	0.364	0.479	0.455	0.545

	HapMap-YRI	Sub-Saharan African	118	IG	0.085	0.186	0.729	0.010	0.178	0.822

	CHMJ	Asian	74	IG					0.351	0.649

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss23799214	70
ss48403838	38	10	10	10
ss74175	1204	194	511	475

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs729421	1301	204	521	485

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
215	ss74175	N/N	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r27_ch14_CEU_illumina:human_1m_beadchip	839538
215	ss23799214	C/T	PERLEGEN	AFD_EUR_PANEL	NA10857		71_IND_CHR_14
263	ss74175	A/G	CSHL-HAPMAP	HapMap-CEU	NA11830	CEPH1350.11	r27_ch14_CEU_illumina:human_1m_beadchip	839538
366	ss74175	G/G	CSHL-HAPMAP	HapMap-CEU	NA10863	CEPH1375.02	r27_ch14_CEU_illumina:human_1m_beadchip	839538

Genotype data submitted for	1316	samples from	1301	individuals	Individual with multiple genotypes submission:	15

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 .