Reference SNP(refSNP) Cluster Report: rs873312

Reference SNP(refSNP) Cluster Report: rs873312

refSNP ID: rs873312
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/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_198570.2:c.826+2317G>C
NT_030008.6:g.1607350G>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1297050 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs873312 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss1297050	TSC-CSHL\|TSC0202622		fwd/T	C/G	atcaatgcaatattaaaacaaactgtgaat	tctgggtatataatatttataaagtgttta	09/06/00	10/10/03	86	Genomic			95 %

Fasta sequence (Legend)

 ACATATTCAT CTCCCTTCTA AAAATCTGTA ATGGGCCACC ACAAAATCTT GCCTTATTCC
 ATCCCATACT GCCTCTCAAA ATATAGAGTT AAAGGGTCAA CATTTAGAAG TTTACCATCA
 GGACAACAAC CGTCTCCCAA AACCATCAAT GCAATATTAA AACAAACTGT GAAT
 S
 TCTGGGTATA TAATATTTAT AAAGTGTTTA GTTTTTGTAC ATTTTTTTAC TCAAAAATAT
 AACTATATCT TAAATGAAAA AATTGAACAC AGAAATAAAT TACTTCTTTG TAAATTTAAC
 ATCTCTGCAC ACTTTTAAGT ATTAATTCAA GTAACTGCTC AATGTAGTTC TCTGACTGTA
 TGCTCTAAGA AGGATAAATC CTAAGGGCAA AAGAAAAACT CTAAAAAAAT CTTGAACACT
 ATTCAGTA

GeneView

GeneView via analysis of contig annotation: VWC2 von Willebrand factor C domain containing 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_030008->NM_198570

function

HuRef

NW_001839006->NM_198570

function

Celera

NW_923273->NM_198570

function

CRA_TCAGchr7v2

NT_079592->NM_198570

function

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


reference	NT_030008->NM_198570->NP_940972	1607350	forward	intron

HuRef	NW_001839006->NM_198570->NP_940972	527999	reverse	intron

Celera	NW_923273->NM_198570->NP_940972	5763590	forward	intron

CRA_TCAGchr7v2	NT_079592->NM_198570->NP_940972	49831900	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs873312 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839006.2	527999	49725720	plus	C	alt_assembly_8	HuRef	HuRef	view	174
7	NT_030008.6	1607350	49815299	minus	G	ref_assembly	reference	reference	view	174
7	NT_079592.2	49831900	49881900	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	174
7	NW_923273.1	5763590	49938940	minus	G	alt_assembly_1	Celera	Celera	view	174

NCBI Resource Links

Submitter-Referenced
GenBank
AC009645.3 AC023199.2 AC034145.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC034145.5 NC_000007.12	AC023199.2

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	HWP	C
ss1297050	HapMap-CEU	European	120	IG	1.000		1.000

	HapMap-HCB	Asian	90	IG	1.000		1.000

	HapMap-JPT	Asian	90	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000		1.000

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