Reference SNP(refSNP) Cluster Report: rs890977

Reference SNP(refSNP) Cluster Report: rs890977

refSNP ID: rs890977
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_004174.1:c.1761-123A>G
NT_006576.15:g.466910T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52082995 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs890977 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
ss1320074	TSC-CSHL\|TSC0161398	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	09/06/00	10/25/06	86	Genomic	95 %
ss3229623	YUSUKE\|IMS-JST039707	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	09/05/01	10/10/03	100	Genomic	unknown
ss3595806	SC_JCM\|AC010442.4_84536	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	09/24/01	10/10/03	100	Genomic	unknown
ss11724234	WI_SSAHASNP\|chr5.NT_023089.13_459648	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	07/03/03	10/10/03	116	Genomic	unknown
ss22276279	SSAHASNP\|WGSA-200403-chr5.chr5.NT_023089.13_459648	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	03/21/04	03/21/04	121	Genomic	unknown
ss52082995	SI_EXO\|NT_006576.15_466910	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	03/29/06	08/14/07	127	Genomic	unknown
ss76865560	CGM_KYOTO\|5622	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	09/12/07	09/12/07	129	cDNA	unknown
ss92956183	BCMHGSC_JDW\|JWB-1921444	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	02/26/08	03/03/08	129	Genomic	unknown
ss95210421	CNG\|17444991	fwd/B	C/T	gctgcctcctgcgtgcccctcgccttccca	ggtgggcacccggctggggcacggggacat	03/13/08	03/13/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGAGGTCACA GCTGTGCCCA CCGCCGGACA TTCTCGCCCT CCTGCCGCAG GAGCTGAGCA
 CGGATCCCCC GTGGTCCCAG GAGGGGACGA GGAAGCCGCC CCACGGGGTC CCTGCGGGGT
 CCTCCAGCCC CCAGCCCGCA GTGCCCACCT CCTGCCGCGG CTTGTACAGG TACTGCTGTA
 GCGTGTGGTG CGTGACCATG TCCTCCGCGT CCCGGATGCT CCGCCGTCGC TGCTCCAGAG
 ACTGCATGTC CAGGCAGACA GCGCTGACAT TTTCTCTCCT GCGTGGGGAC CAGCGCTGAG
 CCATACAGGC TCCCTCAGGG TGGGGTCTCT TGCGCGCCCC TCGCCTTCCC ACGGCGGGCA
 TCTGGCCCTG GCTGCCTCCT GCGTGCCCCT CGCCTTCCCA
 Y
 GGTGGGCACC CGGCTGGGGC ACGGGGACAT CTGCCATCTG GCCAGCCCCT TCTCCCCTCG
 GGGCTTAGGC TGACTCCCCA CGAGGCCTTC CTGGCCTCCT GTCTGAAGTG GGTCCCTTTC
 CTTACTGGTC CCTCTCCAAA GCCCTGGCTG TAAGACTCGG GGACCCCAGC ATCTGCACAT
 CTGGCAGAGT GGACCTCCTA TGAGAACTGG CTGTGAGCTG TGGAGCCCAG GGCCGGAGGA
 GCAGTAAGGG TGGCATGGGG ACCAGGACAG GCTGCTGCGG GCCAGGGGCA AACACGTCAG
 GCCTGGCCCC CAGTCCGCTG CTGCCCCTCC CTTTCACCTT CCATCCAGCA CTAAGGGAGT
 CTGGCCACGG CCTAATATAG GAGGGCTTGT GGAAGGAGAC

GeneView

GeneView via analysis of contig annotation: SLC9A3 solute carrier family 9 (sodium/hydrogen exchanger), member 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_006576->NM_004174

function

HuRef

NW_001838923->NM_004174

function

Celera

NW_922496->NM_004174

function

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


reference	NT_006576->NM_004174->NP_004165	466910	reverse	intron

HuRef	NW_001838923->NM_004174->NP_004165	1658931	forward	intron

Celera	NW_922496->NM_004174->NP_004165	461996	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs890977 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_001838923.2	1658931	464040	minus	G	alt_assembly_8	HuRef	HuRef	view	400
5	NT_006576.15	466910	529910	plus	T	ref_assembly	reference	reference	view	400
5	NW_922496.1	461996	574068	plus	C	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023089 AC084098

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
ss3229623	JBIC-allele		1296	AF					0.522	0.478

ss52082995	HapMap-CEU	European	114	IG	0.772	0.211	0.018		0.877	0.123

	HapMap-HCB	Asian	88	IG	0.250	0.545	0.205		0.523	0.477

	HapMap-JPT	Asian	88	IG	0.159	0.636	0.205		0.477	0.523

	HapMap-YRI	Sub-Saharan African	118	IG	1.000				1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.375+/-0.217	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 .