Reference SNP(refSNP) Cluster Report: rs692200

Reference SNP(refSNP) Cluster Report: rs692200

refSNP ID: rs692200
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002115.1:c.1857+668A>C
NT_023133.12:g.21122921T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss80313842 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs692200 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
ss865982	SC_JCM\|AC034209.2_252330	fwd/T	A/C	caacagttgcattcttagacacctgtgatc	atgaaaagcttcatctcacctactccaacc	07/28/00	10/10/03	83	Genomic	unknown
ss885172	KWOK\|OVLP-000804-72646	fwd/T	A/C	caacagttgcattcttagacacctgtgatc	atgaaaagcttcatctcacctactccaacc	09/01/00	10/10/03	86	Genomic	99 %
ss1578758	KWOK\|OVLP-000925-132449	fwd/T	A/C	caacagttgcattcttagacacctgtgatc	atgaaaagcttcatctcacctactccaacc	10/04/00	04/07/04	87	Genomic	99 %
ss42574958	ABI\|hCV1036533	fwd/T	A/C	caacagttgcattcttagacacctgtgatc	atgaaaagcttcatctcacctactccaacc	07/18/05	07/18/05	126	Genomic	unknown
ss75227752	ILLUMINA\|ILMN_Human_1M_rs692200	fwd/T	A/C	caacagttgcattcttagacacctgtgatc	atgaaaagcttcatctcacctactccaacc	08/28/07	08/29/07	129	Genomic	unknown
ss76639040	AFFY\|AFFY_6_1M_SNP_A-8500179	fwd/T	A/C	ttagacacctgtgatc	atgaaaagcttcatct	08/28/07	08/30/07	129	Genomic	unknown
ss80313842	HGSV\|Cor18507_SNV_20070510.chr5_176245941	rev/B	G/T	ggttggagtaggtgagatgaagcttttcat	gatcacaggtgtctaagaatgcaactgttg	11/23/07	11/25/07	130	Genomic	unknown

Fasta sequence (Legend)

 TTTGGCCTCT CTCCTCCTCC TTTCTTTGTT TCCTTCTCAG TGCCTGGCTC AGTGTTGGGT
 GCATGACTAG GGTGGCAGAG TGCCAGGCAC AGGCTAAGAC ACACATCCCT ACTCAGCACA
 CACTTTAGCT TGTTCTTACA CAAGGATGAG GGACTTCTCA ATGTGCACAC CGGAAGCCTG
 TCACGGAAAC AATACCTCCC GGGCCTCTGG TCCAAACTCC CAGGAATCTC CCTTTCAACA
 TACCCAACTT CTGCTTGAAA GCCTCTTGCC AAGGAGCTCA CTGCCCCTGA AGGCAACAGT
 TGCATTCTTA GACACCTGTG ATC
 M
 ATGAAAAGCT TCATCTCACC TACTCCAACC AGCCTCCATG TGATTTTCAC CCCCTGCTCC
 TGCTCTGACC TCTCTCTGAT ATGCAACTCA TTTTTTTTTT TGAGATGAAG TCTCACTCTG
 TCGCCCAGGT TGGAGTGCAA TGGCATGATC TTGGCTCACT CACTGCAGCC TCCACCTCCT
 GTGTTCAAGC AATCCTCCTG CCTCAGCCTC CCAAGTAGCT GGGACTACAG GCACATGCCA
 ACACGCCCAG CTCATTTTTA GTAGAGATGG GGTTTCACCA TGTTGGCCAG GCTGATCTAG
 AAATCCTGAT CTCAGGTGAT CCGCTCACCT CAGCCTCTCA AAGTTCTGGG ATTACAGGCG
 TGAGCCACCG CACTCCACCT GATATGCAAC TCTGTACTCT GCTTTCTTTT ACACGGTGGT
 CCTTTGGATG GTGCAGTGGG CCAGTCTTGC TGCTTGGCTG CTCTGCTCCA GGCTAAGCCT
 GCTCAGTCCT TTTGATTATT

GeneView

GeneView via analysis of contig annotation: HK3 hexokinase 3 (white cell)

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_023133->NM_002115

function

HuRef

NW_001838960->NM_002115

function

Celera

NW_922796->NM_002115

function

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


reference	NT_023133->NM_002115->NP_002106	21122921	reverse	intron

HuRef	NW_001838960->NM_002115->NP_002106	785126	forward	intron

Celera	NW_922796->NM_002115->NP_002106	761318	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs692200 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838960.2	785126	171236059	plus	A	alt_assembly_8	HuRef	HuRef	view	200
5	NW_922796.1	761318	172188887	plus	A	alt_assembly_1	Celera	Celera	view	200
5	NT_023133.12	21122921	176245941	minus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AC034209 AC012283 AC034209.3

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss1578758	TSC_42_AA		83	AF					0.699	0.301

	TSC_42_C		83	AF					0.916	0.084

	TSC_42_A		84	AF					1.000

	HapMap-CEU	European	118	IG	0.949	0.051		1.000	0.975	0.025

	HapMap-HCB	Asian	82	IG	1.000				1.000

	HapMap-JPT	Asian	86	IG	0.953	0.047		1.000	0.977	0.023

	HapMap-YRI	Sub-Saharan African	108	IG	0.481	0.407	0.111	1.000	0.685	0.315

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.178+/-0.240	270	210	0	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 .