Reference SNP(refSNP) Cluster Report: rs13961

Reference SNP(refSNP) Cluster Report: rs13961

refSNP ID: rs13961
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/C
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_031898.1:c.1362A>C
NP_114104.1:p.T454T
NT_010718.15:g.14804712T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48425947 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13961 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
ss16323	CGAP-GAI\|61848	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	08/23/99	10/10/03	52	cDNA	99 %
ss298718	KWOK\|OVLP-000621-308248	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	06/30/00	10/10/03	85	Genomic	97 %
ss541758	SC_JCM\|AC021300.3_97696	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	07/12/00	05/16/04	80	Genomic	unknown
ss1021265	KWOK\|OVLP-000804-292906	fwd/T	A/C	cctgcagtcgctggtccacatcaaagccac	ctcgagtatgacctggctgtcaaagccaat	09/02/00	10/10/03	86	Genomic	97 %
ss1520275	LEE\|290387	fwd/T	A/C	cctgcagtcgctggtccacatcaaagccac	ctcgagtatgacctggctgtcaaagccaat	09/13/00	10/10/03	86	cDNA	unknown
ss1842321	KWOK\|OVLP-000925-662238	fwd/T	A/C	cctgcagtcgctggtccacatcaaagccac	ctcgagtatgacctggctgtcaaagccaat	10/05/00	10/10/03	87	Genomic	97 %
ss3248416	YUSUKE\|IMS-JST058501	fwd/T	A/C	cctgcagtcgctggtccacatcaaagccac	ctcgagtatgacctggctgtcaaagccaat	09/05/01	10/10/03	100	Genomic	unknown
ss4412109	LEE\|e290387	fwd/T	A/C	cctgcagtcgctggtccacatcaaagccac	ctcgagtatgacctggctgtcaaagccaat	04/26/02	10/10/03	106	cDNA	unknown
ss5613641	SC_JCM\|NT_010718.10_6680388	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	01/10/03	10/10/03	111	Genomic	unknown
ss10869860	BCM_SSAHASNP\|chr17.NT_010718.13_14046501	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	06/30/03	10/10/03	116	Genomic	unknown
ss16746632	CSHL-HAPMAP\|CSHL-HuAA-200402.chr17.NT_010718.14_14048370	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	02/17/04	03/04/04	120	Genomic	unknown
ss17584039	CSHL-HAPMAP\|CSHL-HuCC-200402.chr17.NT_010718.14_14048370	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	02/19/04	03/04/04	120	Genomic	unknown
ss21379452	SSAHASNP\|WGSA-200403-chr17.chr17.NT_010718.14_14048370	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	03/19/04	03/19/04	123	Genomic	unknown
ss23637858	PERLEGEN\|afd3713685	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	08/10/04	09/13/04	123	Genomic	unknown
ss24792366	SEQUENOM\|sqnm106112	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	06/18/04	06/18/04	126	cDNA	unknown
ss28507286	MGC_GENOME_DIFF\|BC031688x37543500-T14048370G	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	08/25/04	08/25/04	126	cDNA	unknown
ss48425947	APPLERA_GI\|hCV774426	fwd/T	A/C	cctgcagtcgctggtccacatcaaagccac	ctcgagtatgacctggctgtcaaagccaat	09/28/05	11/03/06	126	Genomic	unknown
ss75041015	ILLUMINA\|ILMN_Human_1M_rs13961	fwd/T	A/C	cctgcagtcgctggtccacatcaaagccac	ctcgagtatgacctggctgtcaaagccaat	08/28/07	08/29/07	129	Genomic	unknown
ss76535692	AFFY\|AFFY_6_1M_SNP_A-8396766	fwd/T	A/C	tccacatcaaagccac	ctcgagtatgacctgg	08/28/07	08/30/07	129	Genomic	unknown
ss78722227	HGSV\|Cor18507_SNV_20070510.chr17_15148089	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	10/19/07	10/20/07	129	Genomic	unknown
ss82486051	HGSV\|Cor19240_SNV_20070510.chr17_15148089	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	11/30/07	12/02/07	130	Genomic	unknown
ss90545881	BCMHGSC_JDW\|JWB-1006058	rev/B	G/T	attggctttgacagccaggtcatactcgag	gtggctttgatgtggaccagcgactgcagg	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATTCCCATTG GTTCATTGTC ACCATTCTCT TTATATTTCT TTATATTTTA TTAATTTCAT
 GCACCTCTCA TTTGCTGATA AATATATCCT AAAGTAAAGA AAATGTGAGC TTTGCATCGC
 TGGTTACAAT GTGATGTACT TGGAGTTGCG TAAGCTACAT GCTGACCTAA CCATGCTGAT
 TCCTTTATGC TGCAGCCTTG TTAACGAGGT ACACGAGGTT GACGACACCA TCCAGACCCT
 GCAGCAGCGC CTGAGGGATG CAGAGGACAC CCTGCAGTCG CTGGTCCACA TCAAAGCCAC
 M
 CTCGAGTATG ACCTGGCTGT CAAAGCCAAT TCCCTGTACA TCGACCAGGA AAAATGCATG
 AGCATGCGCA AGAGCTACCC CAACACCCTC CGGCTGGTCG GCTTCTGCTA GGGACCCCAC
 CGGGTGTGGT TTTGATACCC CTAAGTTAAG GCTGAGCCAG AGCACTGTCT CAGCATTTGA
 ACCGAATGCT AATATAGTCA CTTATTAAAG GATTATGCTG ATGGAAATGT ACCAACCTCC
 TGTCTCGGAA AGCCTTTTGT TTGCATCCAA ACCTTAATTT TCTATTATTT ACTAGGCGTC

GeneView

GeneView via analysis of contig annotation: TEKT3 tektin 3

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_010718->NM_031898

function

HuRef

NW_001838403->NM_031898

function

Celera

NW_926584->NM_031898

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_010718->NM_031898->NP_114104	14804713	reverse	1461	synonymous	C	Thr [T]	3	454
					contig reference	A	Thr [T]	3	454

HuRef	NW_001838403->NM_031898->NP_114104	14792152	reverse	1461	synonymous	A	Thr [T]	3	454
					contig reference	C	Thr [T]	3	454

Celera	NW_926584->NM_031898->NP_114104	15149440	reverse	1461	synonymous	A	Thr [T]	3	454
					contig reference	C	Thr [T]	3	454

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs13961 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838403.1	14792152	15100982	minus	G	alt_assembly_8	HuRef	HuRef	view	300
17	NT_010718.15	14804713	15148089	minus	T	ref_assembly	reference	reference	view	300
17	NW_926584.1	15149440	15231944	minus	G	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm106112	NT_010718.10 AA782924 AC005703 AC021300.3 BC031688 Hs.47152

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC005703.2 NC_000017.9	AC021300.4

UniGene Cluster ID
414648

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss23637858	AFD_EUR_PANEL	European	48	IG	0.042	0.417	0.542	0.655	0.250	0.750

	AFD_AFR_PANEL	African American	46	IG	0.087	0.348	0.565	0.655	0.261	0.739

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.250	0.625	0.150	0.250	0.750

ss48425947	HapMap-CEU	European	120	IG	0.050	0.333	0.617		0.217	0.783

	HapMap-HCB	Asian	90	IG	0.133	0.289	0.578		0.278	0.722

	HapMap-JPT	Asian	90	IG	0.089	0.289	0.622		0.233	0.767

	AGI_ASP population	African American	72	IG	0.028	0.389	0.583	0.479	0.222	0.778

ss541758	CEPH		184	AF					0.190	0.810

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.366+/-0.221	281	239	9	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .