Reference SNP(refSNP) Cluster Report: rs6955338

Reference SNP(refSNP) Cluster Report: rs6955338

refSNP ID: rs6955338
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
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
NM_001042482.1:c.355-494G>A
NM_022445.3:c.502-494G>A
NT_007914.14:g.4822205C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10373673 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6955338 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss10373673	BCM_SSAHASNP\|chr7.NT_007914.12_4788960		fwd/B	C/T	ctctgttgccgaggctggagtgcaatgttg	aatcttggctcactgcaacctctgccgcca	06/29/03	10/10/03	116	Genomic			unknown
ss114573206	1000GENOMES\|NA19240_2008_12_16_1689211_chr7_143877122		fwd/B	C/T	ctctgttgccgaggctggagtgcaatgttg	aatcttggctcactgcaacctctgccgcca	12/18/08	12/18/08	130	Genomic			unknown

Fasta sequence (Legend)

 AACTATGAGA AAATTGAAGC TTGCAGAGAT TAACATAGGA CCACACAGAT AAGGGATTCC
 TACCTACACC TGCCAATTCC AGAGACCAAA CTCACAGCAA TAGGACTGTG GGTTTGAAAC
 CTATCCTAAA TGAAAGGTAC CACACAAAGA GAAACACACA AAGACAGCTG CTTCTCAGCA
 GCCATTACAA TGTATTCTGC tttttttttt tttttctttt ttaagatgga gtctcactct
 gttgccgagg ctggagtgca atgttg
 Y
 aatcttggct cactgcaacc tctgccgcca gggttcaagc aattctcctg cctcctgagt
 agctaggact acaggcgggc accaccacac ccagctaatt ttatattttt agtagagatg
 gggtttcacc acattggcca ggctggtctc gaactcctga cctcaagtga tccacccacc
 tcagcctccc aaagtgctgg gattgcaggc atgagccacg acacctggcc TTGCGTTTtt
 tgtttgtttg cttgtttgtt tTCCTAAAAA AGTTTTTATT TTCTTTTAGG TAAGAGCTGC
 CTTTATTCCT TTTGTATAGA ATTCCTCCCC GCCCCAAGTT GATTTATATT GAATAGCTTG
 CCACACAAAT TTGAGATTTG TTTCTTCCTA CCATTCTCCA TTATATAAAT AATTCTCTCT
 GAAGACAGAT ATACTAAACA TAATACAAAT GAC

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	4822205	reverse	intron

reference	NT_007914->NM_022445->NP_071890	4822205	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6955338 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	204730	138324249	plus	C	alt_assembly_8	HuRef	HuRef	view	266
7	NW_923707.1	186430	138920253	plus	C	alt_assembly_1	Celera	Celera	view	266
7	NT_079596.2	43620040	143584472	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	266
7	NT_007914.14	4822205	143877122	plus	C	ref_assembly	reference	reference	view	266

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007914

dbSNP Blast Analysis

Population Diversity

There is no frequency data.

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 .