Reference SNP(refSNP) Cluster Report: rs6456880

Reference SNP(refSNP) Cluster Report: rs6456880

refSNP ID: rs6456880
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_001010877.2:c.1531A>C
NP_001010877.2:p.K511Q
NT_007592.14:g.19821498T>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss12676690 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6456880 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
ss10307137	BCM_SSAHASNP\|chr6.NT_007592.13_19821509	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	06/29/03	10/10/03	116	Genomic	unknown
ss11804158	WI_SSAHASNP\|chr6.NT_007592.13_19821509	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	07/04/03	10/10/03	116	Genomic	unknown
ss12676690	SI_MHC_SNP\|AL662791.3_30203_TG	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	09/10/03	10/25/06	118	Genomic	unknown
ss13095770	SC_SNP\|NT_007592.13_19821509	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	10/22/03	10/31/03	119	Genomic	unknown
ss13149080	SC_SNP\|NT_033951.3_418554	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	10/22/03	10/31/03	119	Genomic	unknown
ss17135946	CSHL-HAPMAP\|CSHL-HuAA-200402.chr6.NT_007592.13_19821509	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	02/17/04	03/04/04	120	Genomic	unknown
ss24338016	PERLEGEN\|afd0288236	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	08/10/04	09/13/04	123	Genomic	unknown
ss42767402	ABI\|hCV25927604	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	07/18/05	07/18/05	126	Genomic	unknown
ss66622523	ILLUMINA\|HumanHap300v1.1_rs6456880	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	11/09/06	11/09/06	127	Genomic	unknown
ss67456526	ILLUMINA\|HumanHap550v1.1_rs6456880	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	11/14/06	11/14/06	127	Genomic	unknown
ss67809163	ILLUMINA\|HumanHap650Yv1.0_rs6456880	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	11/14/06	11/14/06	127	Genomic	unknown
ss68970104	PERLEGEN\|PGP00288236	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	01/30/07	03/31/08	127	Genomic	unknown
ss70865392	ILLUMINA\|HumanHap550v3.0__rs6456880	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	04/20/07	03/31/08	130	Genomic	unknown
ss71453342	ILLUMINA\|HumanHap650Yv3.0_rs6456880	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	04/23/07	04/23/07	127	Genomic	unknown
ss71648369	SI_EXO\|NT_007592.14_19821499	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	05/07/07	05/07/07	127	Genomic	unknown
ss75439780	ILLUMINA\|ILMN_Human_1M_rs6456880	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	08/28/07	08/29/07	129	Genomic	unknown
ss77535406	HGSV\|Cor12156_SNV_20070510.chr6_29071227	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	10/09/07	10/13/07	129	Genomic	unknown
ss79009376	HGSV\|Cor18507_SNV_20070510.chr6_29071227	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	10/19/07	10/21/07	129	Genomic	unknown
ss79220991	ILLUMINA\|HumanHap300v2.0_rs6456880	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	04/18/07	11/18/07	130	Genomic	unknown
ss84480583	KRIBB_YJKIM\|KHS721336	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	12/04/07	12/07/07	130	Genomic	unknown
ss86259029	CORNELL\|hCV25927604	fwd/T	A/C	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	01/21/08	01/21/08	129	Genomic	unknown
ss93429833	BCMHGSC_JDW\|JWB-2114832	fwd/B	G/T	ggattctctgatggatggtaaggcagtgct	atcttggaaggttttcccacaatccctgca	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCATCAAGTT CATGGGTACT CCATACTTGA TGTTTTCTTT TCTTATGTCC AGTAAGATTT
 GAGCTCACTC TAAAAGCTTT TCCACATTCC TCACATTCAT AAGGTTTCTC CCCAGTATGA
 ACTCGCTTAT GTCCAATCAG AGCTGAGCCC TGACGGAAGG ACGTGCCACA CTCACTGCAG
 GTGTATGGCT TCTCACCAGT GTGGATTCTT TTGTGCTGCC TCAGGACTGA ACTATGATGG
 AAGGCCATTC CACATACCTC ACATTTGTGA GGCTTCTCTC CAGTGTGAAT TCTTCGATGA
 TTGGTCAAGT TTGACTTCCC ACTGAAAGCT TTCCCACACT CTAAACATTT GTAAGGTTTC
 TCTCCAGTGT GGATTCTCTG ATGGATGGTA AGGCAGTGCT
 K
 ATCTTGGAAG GTTTTCCCAC AATCCCTGCA TTGATAGGGC TTCTCCCCTG TATGCTCTCG
 TTCATGAGCC CTGCGCTTAC AGTTATGACG AAAGGCTTTC CCACACTCCT CACACCTGTA
 ACGTTTCTCT TCAGTGTGGA TCCTTCTGTG TTTGGTGAGT TCTGCCTTGA TGCTGAAGTC
 TTTTCCACAC TGGGGACACC CATAGTGTTT CTCCCGAGTA TGGATTCGTT TGTGTTTGCT
 TAGGTCTGAG CTCCGACTGA AGGCCCTTCC ACACTTGCTG CACTCATAAG GTCGTTCCCC
 AGTGTGGATT CTTATGTGTT TGGTGAGGTC TGAACTCCCA CTGAAGGCCT TCCCGCACTC
 CTCACATTCA TATGGCTTCT CCCCAGTGTG GATTCTGCCA

GeneView

GeneView via analysis of contig annotation: ZNF311 zinc finger protein 311

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_007592->NM_001010877

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_007592->NM_001010877->NP_001010877	19821499	reverse	2044	missense	C	Gln [Q]	1	511
					contig reference	A	Lys [K]	1	511

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6456880 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_001838980.1	2042960	28770651	plus	T	alt_assembly_8	HuRef	HuRef	view	400
6	NT_007592.14	19821499	29071227	plus	T	ref_assembly	reference	reference	view	400
6	NT_113892.1	220592	29106101	plus	T	alt_assembly_4	c6_QBL	c6_QBL	view	400
6	NT_113891.1	418554	29107097	plus	T	alt_assembly_3	c6_COX	c6_COX	view	400
6	NW_923073.1	2033679	30569358	plus	T	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033951

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank mRNA:
NM_001010877.2	AL662791.3 AL662865.4 AL929561.5 BX293545.10 BX927167.6 CR759835.5 CR759957.2 Z84476.7	BX537150.3 CR759862.3 CT009516.2	AK289881.1

UniGene Cluster ID
148218

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	N	T
ss12676690	HapMap-CEU	European	120	IG	0.167	0.433	0.400	0.527	0.383		0.617

	HapMap-HCB	Asian	90	IG	0.400	0.489	0.111	0.655	0.644		0.356

	HapMap-JPT	Asian	88	IG	0.432	0.523	0.045	0.150	0.693		0.307

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

	CHMJ	Asian	74	IG					0.568	0.014	0.419

ss24338016	AFD_EUR_PANEL	European	48	IG	0.167	0.458	0.375	1.000	0.396		0.604

	AFD_AFR_PANEL	African American	46	IG	0.783	0.174	0.043	0.273	0.870		0.130

	AFD_CHN_PANEL	Asian	48	IG	0.375	0.542	0.083	0.371	0.646		0.354

ss68970104	HapMap-CEU	European	120	GF	0.167	0.433	0.400		0.383		0.617

	HapMap-HCB	Asian	90	GF	0.400	0.489	0.111		0.644		0.356

	HapMap-JPT	Asian	90	GF	0.444	0.511	0.044		0.700		0.300

	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
	0.444+/-0.158	332	260	270	0

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 .