Reference SNP(refSNP) Cluster Report: rs2305668

Reference SNP(refSNP) Cluster Report: rs2305668

refSNP ID: rs2305668
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
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_005697.3:c.632+94A>C
NT_010194.16:g.45933079T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss23996133 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2305668 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
ss3252965	YUSUKE\|IMS-JST063050	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	09/05/01	10/10/03	100	Genomic	unknown
ss23996133	PERLEGEN\|afd3560140	rev/B	G/T	aagtggatttccctacattctattctgctc	aagactcagatggggtcccagggcctatag	08/10/04	09/13/04	123	Genomic	unknown
ss66247650	AFFY\|SNP_A-4277340	rev/B	G/T	acattctattctgctc	aagactcagatggggt	10/27/06	08/14/07	127	Genomic	unknown
ss66836704	ILLUMINA\|HumanHap300v1.1_rs2305668	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	11/09/06	11/09/06	127	Genomic	unknown
ss67245367	ILLUMINA\|HumanHap550v1.1_rs2305668	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	11/14/06	11/14/06	127	Genomic	unknown
ss67642394	ILLUMINA\|HumanHap650Yv1.0_rs2305668	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	11/14/06	11/14/06	127	Genomic	unknown
ss70723699	ILLUMINA\|HumanHap550v3.0__rs2305668	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	04/20/07	03/30/08	130	Genomic	unknown
ss71292306	ILLUMINA\|HumanHap650Yv3.0_rs2305668	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	04/23/07	04/23/07	127	Genomic	unknown
ss75893250	ILLUMINA\|ILMN_Human_1M_rs2305668	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	08/28/07	08/29/07	129	Genomic	unknown
ss76393252	AFFY\|AFFY_6_1M_SNP_A-4277340	rev/B	G/T	acattctattctgctc	aagactcagatggggt	08/28/07	08/30/07	129	Genomic	unknown
ss79128928	ILLUMINA\|HumanHap300v2.0_rs2305668	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	04/18/07	11/18/07	130	Genomic	unknown
ss84031127	KRIBB_YJKIM\|KHS607371	fwd/T	A/C	ctataggccctgggaccccatctgagtctt	gagcagaatagaatgtagggaaatccactt	12/04/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCTTTAGGTG AGTGAGGCCG GGGCAAGGGG TGAGACTTTA TGGCTGGCAT CCCAGGTAGC
 AGGCTAAGGG CTATAGGCCC TGGGACCC
 CATCTGAGTC TT
 M
 GAGCAGAATA GA
 ATGTAGGGAA ATCCACTTTC CCTACATTCT GTTCCTCTGT TCCCACCCAG AGCAGAGATT
 GGGGGCCCCG TTCCTCAGTT TCTGTACC

GeneView

GeneView via analysis of contig annotation: SCAMP2 secretory carrier membrane protein 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_010194->NM_005697

function

Celera

NW_925907->NM_005697

function

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


reference	NT_010194->NM_005697->NP_005688	45933079	reverse	intron

Celera	NW_925907->NM_005697->NP_005688	749336	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2305668 maps exactly once on NCBI human chromosome 15

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
15	NW_001838219.1	748548	51939657	minus	T	alt_assembly_8	HuRef	HuRef	view	100
15	NW_925907.1	749336	52092775	minus	T	alt_assembly_1	Celera	Celera	view	100
15	NT_010194.16	45933079	72929814	minus	T	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000015.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC091230.23 AC125435.8 NC_000015.8	AC020705.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C	N
ss23996133	AFD_EUR_PANEL	European	48	IG	0.750	0.250		0.527	0.875	0.125

	AFD_AFR_PANEL	African American	44	IG	0.909	0.091		1.000	0.955	0.045

	AFD_CHN_PANEL	Asian	48	IG	0.542	0.458		0.150	0.771	0.229

	HapMap-CEU	European	120	IG	0.767	0.217	0.017	1.000	0.875	0.125

	HapMap-HCB	Asian	90	IG	0.511	0.422	0.067	0.752	0.722	0.278

	HapMap-JPT	Asian	90	IG	0.467	0.444	0.089	0.584	0.689	0.311

	HapMap-YRI	Sub-Saharan African	120	IG	0.933	0.067		1.000	0.967	0.033

	CHMJ	Asian	74	IG					0.649	0.297	0.054

ss3252965	JBIC-allele		1496	AF					0.678	0.322

ss66247650	HapMap-CEU	European	118	GF	0.763	0.220	0.017		0.873	0.127

	HapMap-HCB	Asian	90	GF	0.511	0.422	0.067		0.722	0.278

	HapMap-JPT	Asian	90	GF	0.467	0.444	0.089		0.689	0.311

	HapMap-YRI	Sub-Saharan African	120	GF	0.933	0.067			0.967	0.033

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.278+/-0.248	332	260	269	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .