Reference SNP(refSNP) Cluster Report: rs17169931

Reference SNP(refSNP) Cluster Report: rs17169931

refSNP ID: rs17169931
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
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_001042482.1:c.466+17696A>G
NM_022445.3:c.613+17696A>G
NT_007914.14:g.4803904T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43052957 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17169931 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
ss23540681	PERLEGEN\|afd0538302	fwd/B	C/T	tccctgttgagggcatcaaataaatcctac	tgcaaaatttgttttgtttatgtcttgatt	08/10/04	09/13/04	123	Genomic	unknown
ss43052957	ABI\|hCV2965410	fwd/B	C/T	tccctgttgagggcatcaaataaatcctac	tgcaaaatttgttttgtttatgtcttgatt	07/18/05	11/03/06	126	Genomic	unknown
ss93781867	BCMHGSC_JDW\|JWB-2386000	fwd/B	C/T	tccctgttgagggcatcaaataaatcctac	tgcaaaatttgttttgtttatgtcttgatt	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 GATTGCTGCC TGTTATTGGT ATAAAGTATC AGTCTCTCGT ATAAGAACAA CTTAAAAAGG
 CTAAAAACAG AAAAGACATG CAAAAAGGCT GGGAAACATA TGTCTAAGAA GAGACTGGAT
 AAAACCTGCC ACAGAGTGAA GAGTGAGCTC TAGCCTAAGT AAACCTGCTG ACTTCCTTCC
 TGGTTCTGAA GCATCAAAAT ACACACGTGG CAAAACTTAC TACAATTTTG GAGAACAGTA
 ACTACATTGA ATGGAAAAGG TAGACCTCAT TCCCTGTTGA GGGCATCAAA TAAATCCTAC
 Y
 TGCAAAATTT GTTTTGTTTA TGTCTTGATT CTTAACTGCA AGTTACCTGA GGCAAGATGA
 ATGACAACAC TAAGTTTTTC AAATAGAATA CAATTATATA CCGTTTTTAT ACATCGATTC
 AATTGTACAG ATTCAATGGC ATATAATTGT ATTCAAGAAG TATTATTTTA GAAAATCACT
 GGATTACTAT CTGATATAGT AGGCTGAATA ATGGACCACT AAAAAGTCCT CAATTGTAAT
 CCCCGGAACC TGCCAATATG CTACTTACAT GGCAAGAGGA ACTTTACAGA TGTGATTAAG

GeneView

GeneView via analysis of contig annotation: TPK1 thiamin pyrophosphokinase 1

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_007914->NM_001042482

function

reference

NT_007914->NM_022445

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_007914->NM_001042482->NP_001035947	4803904	reverse	intron

reference	NT_007914->NM_022445->NP_071890	4803904	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17169931 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839078.1	186430	138305949	plus	T	alt_assembly_8	HuRef	HuRef	view	300
7	NW_923707.1	168128	138901951	plus	T	alt_assembly_1	Celera	Celera	view	300
7	NT_079596.2	43601737	143566169	plus	T	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	300
7	NT_007914.14	4803904	143858821	plus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000007.8

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
ss23540681	AFD_EUR_PANEL	European	48	IG		0.125	0.875	0.752	0.062	0.938

	AFD_AFR_PANEL	African American	46	IG		0.174	0.826	0.655	0.087	0.913

	AFD_CHN_PANEL	Asian	48	IG			1.000			1.000

ss43052957	HapMap-CEU	European	120	IG	0.017	0.100	0.883	0.150	0.067	0.933

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	90	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.183	0.800	0.752	0.108	0.892

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.095+/-0.196	332	260	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 .