Reference SNP(refSNP) Cluster Report: rs2160402

Reference SNP(refSNP) Cluster Report: rs2160402

refSNP ID: rs2160402
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_000834.2:c.1010+13728C>T
NT_009714.16:g.6651497G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38908919 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2160402 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
ss3092161	TSC-CSHL\|TSC1191549	fwd/B	C/T	gggagtacctactgagtgctcagaagtgtg	ggaacagcccaggtattcaccatctctctg	06/07/01	10/25/06	96	Genomic	unknown
ss38908919	ABI\|hCV16079442	rev/T	A/G	cagagagatggtgaatacctgggctgttcc	cacacttctgagcactcagtaggtactccc	07/16/05	11/02/06	126	Genomic	unknown
ss66150095	AFFY\|SNP_A-2130225	rev/T	A/G	atacctgggctgttcc	cacacttctgagcact	10/27/06	08/14/07	127	Genomic	unknown
ss76178261	AFFY\|AFFY_6_1M_SNP_A-2130225	rev/T	A/G	atacctgggctgttcc	cacacttctgagcact	08/28/07	08/30/07	129	Genomic	unknown
ss88982628	BCMHGSC_JDW\|JWB-0522398	rev/T	A/G	cagagagatggtgaatacctgggctgttcc	cacacttctgagcactcagtaggtactccc	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCATGACGCC CGGTGCTACT CAGCAGCGTT CCTTTTCCCT TTGATGTGAT TCCTCTTCAT
 AGCATGATTT AGTGAGAATC TGGCTCAGAG CGGCCTCTAG TGGCTCAATC CTTAGGGATG
 CGCTTCCTTC CCCAGCCCAG TTCCAAATTC AGCCCAGTTC CAAAATTAAC CACCTTAGCC
 AAGTTGGACA CTTGTGTGTT TAGAACCATT CTCCATGCAA TCAGCTATTT TTTTTCAGAA
 TCTTTCTCAT CAGCCACAAG TATTACACCG GGGAGTACCT ACTGAGTGCT CAGAAGTGTG
 Y
 GGAACAGCCC AGGTATTCAC CATCTCTCTG GCCAGGAGAG ACCAGCATTA CCCCAAACAT
 TTGGTGAACA GTAGAGAGCA GTGGCAGGGA AGCTATGTGG TAGAGGCAGT AATGTTGAAT
 AAAGTAATCC CAGTAAAATA GGTTGGTTAG GATCATCAGA AGTTAGCTTT TTTTTTCCTT
 TTCTTCTTTT TTTTTTTTTT TTTTTTTTTT TTTTGAGACG GAGTTTCACT CTTGTTGCCC
 AGGCTGGAGT GCAATGGTGC AATCTCAGCT CACCACAACC TCCGCCTCCT AGGTTCAGCG

GeneView

GeneView via analysis of contig annotation: GRIN2B glutamate receptor, ionotropic, N-methyl D-aspartate 2B

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_009714->NM_000834

function

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


reference	NT_009714->NM_000834->NP_000825	6651497	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2160402 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838052.1	4297389	13657906	minus	G	alt_assembly_8	HuRef	HuRef	view	300
12	NT_009714.16	6651497	13783790	minus	G	ref_assembly	reference	reference	view	300
12	NW_925328.1	4151777	19037093	minus	G	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced

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
ss38908919	HapMap-CEU	European	120	IG	0.867	0.133		0.584	0.933	0.067

	HapMap-HCB	Asian	90	IG	0.733	0.222	0.044	0.317	0.844	0.156

	HapMap-JPT	Asian	88	IG	0.659	0.318	0.023	0.655	0.818	0.182

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

ss66150095	HapMap-CEU	European	118	GF	0.864	0.136			0.932	0.068

	HapMap-HCB	Asian	90	GF	0.733	0.244	0.022		0.856	0.144

	HapMap-JPT	Asian	90	GF	0.667	0.311	0.022		0.822	0.178

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss38908919	269
ss66150095	268

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2160402	270

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5153	ss38908919	A/A	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	r23_ch12_HCB_illumina:golden_gate_1.1.0	797495
5153	ss66150095	A/G	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	chr12-HapMap-HCB

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA, PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .