Reference SNP(refSNP) Cluster Report: rs330868

Reference SNP(refSNP) Cluster Report: rs330868

refSNP ID: rs330868
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_001013399.1:c.-223-2131A>G
NM_005190.3:c.33-2131A>G
NT_025741.14:g.4182412T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss77555428 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs330868 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
ss422617	KWOK\|OVLP-000621-303666	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	06/30/00	10/10/03	79	Genomic	99 %
ss661194	SC_JCM\|AL137784.6_82366	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	07/27/00	10/10/03	87	Genomic	unknown
ss1174265	KWOK\|OVLP-000804-559781	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	09/02/00	10/10/03	86	Genomic	99 %
ss1727611	KWOK\|OVLP-000925-252315	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	10/05/00	10/10/03	87	Genomic	97 %
ss2093278	TSC-CSHL\|TSC0805883	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	10/19/00	10/10/03	88	Genomic	95 %
ss12855972	SC_SNP\|NT_025741.12_4182412	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	10/21/03	10/31/03	119	Genomic	unknown
ss15757703	SC_SNP\|NT_025741.13_4182412	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	11/17/03	11/22/03	120	Genomic	unknown
ss20264341	CSHL-HAPMAP\|CSHL-HuFF-200402.chr6.NT_025741.13_4182412	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	02/21/04	03/04/04	120	Genomic	unknown
ss22393619	SSAHASNP\|WGSA-200403-chr6.chr6.NT_025741.13_4182412	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	03/21/04	03/21/04	121	Genomic	unknown
ss42789898	ABI\|hCV27341532	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	07/18/05	07/18/05	126	Genomic	unknown
ss77555428	HGSV\|Cor12156_SNV_20070510.chr6_100119676	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	10/09/07	10/13/07	129	Genomic	unknown
ss93525803	BCMHGSC_JDW\|JWB-2191521	fwd/B	C/T	cttcttcatatgctgtgctactttaaaaca	agaaaattaagtaattaataggtgatatga	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGCCTTTCCT GATTCAAAAC GATAAAAAAC AATTCACCCA TATTTTCTAA TACCCTTAAG
 AGCTTTTTTC CTTCAATTTA TGATCCATCT GGAATTTATT TTGGTACAGA GTATAAAGCA
 GGGATCCAGC TAAATATGTT GTCAAATGCT TATCCAAATG TGCTAAGGTA TTTCCTGATT
 TATAATTCTA TCATTATACT TGGATCTTCT TTATAATTTC CTATTTTTTT CTTCTTCATA
 TGCTGTGCTA CTTTAAAACA
 Y
 AGAAAATTAA GTAATTAATA GGTGATATGA AAAATACTCC CTTCTATTCT TCTGAAAATT
 TCTGACTATT CTATCACAAT TATTCTAAGA CCTAAACTTT AGAAGCATTA TGTCGAGTCC
 TAAAAAAGAA TATCCATTCA AATTTTGTGA TTACATTACA TTTAAAGATC AATATGGGGA
 GAAATGACAT CTTACCAAGA ATTCAAACTC TATTAAAATC TGTATGTGCC ACTATGGACT
 TTTAAAGTTT TCTTCCTACA GGTTCTGTAT ATTTCTTTAT ATTTTTCCCT CTGTATATTT
 TCTGTTGCTA ATGTAAATTA TACTTCTCTA TCCATTTTTA AAAAGCTTTT ATTTTTGCAT
 TTTATAACTG GTCACCTTC

GeneView

GeneView via analysis of contig annotation: CCNC cyclin C

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_025741->NM_001013399

function

reference

NT_025741->NM_005190

function

HuRef

NW_001838988->NM_001013399

function

HuRef

NW_001838988->NM_005190

function

Celera

NW_923184->NM_001013399

function

Celera

NW_923184->NM_005190

function

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


reference	NT_025741->NM_001013399->NP_001013417	4182412	reverse	intron

reference	NT_025741->NM_005190->NP_005181	4182412	reverse	intron

HuRef	NW_001838988->NM_001013399->NP_001013417	6450210	forward	intron

HuRef	NW_001838988->NM_005190->NP_005181	6450210	forward	intron

Celera	NW_923184->NM_001013399->NP_001013417	32725683	reverse	intron

Celera	NW_923184->NM_005190->NP_005181	32725683	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs330868 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838988.2	6450210	97453280	minus	A	alt_assembly_8	HuRef	HuRef	view	260
6	NT_025741.14	4182412	100119676	plus	T	ref_assembly	reference	reference	view	260
6	NW_923184.1	32725683	100657079	plus	C	alt_assembly_1	Celera	Celera	view	260

NCBI Resource Links

Submitter-Referenced
GenBank
NT_025741 AC025216 AL137784.10 AL357622 AL357622.7

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL137784.14 NC_000006.10	AC025216.2 AL357622.7

Population Diversity

There is no frequency data.

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .