Reference SNP(refSNP) Cluster Report: rs9332315

Reference SNP(refSNP) Cluster Report: rs9332315

refSNP ID: rs9332315
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
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_006440.3:c.103+1025A>G
NT_011519.10:g.3080349T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss12673688 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9332315 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
ss12673688	EGP_SNPS\|COMT-000763	fwd/B	C/T	ttttcctccttttgatgccgaatccccttt	atgggactccgccagcacgggtgcatttaa	08/22/03	03/31/08	119	Genomic	unknown
ss48297530	SNP500CANCER\|TXNRD2-84	rev/T	A/G	ttaaatgcacccgtgctggcggagtcccat	aaaggggattcggcatcaaaaggaggaaaa	08/19/05	11/03/06	126	Genomic	unknown
ss75230774	ILLUMINA\|ILMN_Human_1M_rs9332315	fwd/B	C/T	ttttcctccttttgatgccgaatccccttt	atgggactccgccagcacgggtgcatttaa	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 ggttcagttt gttctttccc ttaaaatagg aagataaggg cattatcccc ctaagtctcg
 tatgatattc cccattctga gtccagaata cctagaaatt tggaatttgg ctattgccgt
 gtctggactg tgagtatggg aaggggaaac ttttctgtct gttgtcccca ctaccgcccc
 tcacatccgt gattctgaac cccatgataa atgccctttg aacctttttc ctccttttga
 tgccgaatcc ccttt
 Y
 atgggactcc gCCAGCACGG GTGCATTTAA CCTTCCTGAG CTTGCCCACC TGACGCATGC
 AGCCAAGAAG CTTTGAAAGA TGGAGTGCCC TGGCTGAGGG TTCCAGGTCT CAGCAAGGCC
 ACGAGGTGGT GACTGCCTCC CAGAACTCTG TTGGGCCACC CTCCGTCCTG GAGACCCCCA
 AAACCTCCAT AGCACCAACT CTGCCCATTC ACACACACAG TCAGCCCTCC CTCCCGAGTC
 CACCGCGGGC AGAGG

GeneView

GeneView via analysis of contig annotation: TXNRD2 thioredoxin reductase 2

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_011519->NM_006440

function

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


reference	NT_011519->NM_006440->NP_006431	3080349	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9332315 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838737.2	396501	3548761	minus	A	alt_assembly_8	HuRef	HuRef	view	255
22	NW_927495.1	1048703	3779475	plus	T	alt_assembly_1	Celera	Celera	view	255
22	NT_011519.10	3080349	18308199	plus	T	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011519

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/T	T/T	HWP	C	T
ss12673688	PDR90	Global	180	IG	0.011	0.989	1.000	0.006	0.994

	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG	0.067	0.933		0.033	0.967

	HapMap-JPT	Asian	90	IG	0.022	0.978		0.011	0.989

	HapMap-YRI	Sub-Saharan African	120	IG		1.000			1.000

ss48297530	P1		188	AF	0.011	0.989	1.000	0.005	0.995

	CAUC1		52	AF		1.000			1.000

	AFR1		46	AF		1.000			1.000

	HISP1		44	AF		1.000			1.000

	PAC1		46	AF	0.043	0.957	1.000	0.022	0.978

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.014+/-0.083	360	300	0	0

Validation Summary:

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

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Revised: May 25, 2006 1:38 PM .