Reference SNP(refSNP) Cluster Report: rs4464911

Reference SNP(refSNP) Cluster Report: rs4464911

refSNP ID: rs4464911
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
Map to Genome Build:	36.3

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

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss19732107 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4464911 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
ss5996626	SC_JCM\|NT_030008.5_1459064	fwd/T	A/G	tcctgttcctgatttttcacttctctcttt	ctaacagtgttgaaaatctccacacaggtt	01/10/03	10/10/03	111	Genomic	unknown
ss19732107	CSHL-HAPMAP\|CSHL-HuDD-200402.chr7.NT_030008.6_1459064	fwd/T	A/G	tcctgttcctgatttttcacttctctcttt	ctaacagtgttgaaaatctccacacaggtt	02/20/04	10/26/06	120	Genomic	unknown
ss43048234	ABI\|hCV11581822	fwd/T	A/G	tcctgttcctgatttttcacttctctcttt	ctaacagtgttgaaaatctccacacaggtt	07/18/05	07/18/05	126	Genomic	unknown
ss66346000	AFFY\|SNP_A-1957920	rev/B	C/T	ttttcaacactgttag	aaagagagaagtgaaa	10/29/06	03/31/08	127	Genomic	unknown
ss76053972	AFFY\|AFFY_6_1M_SNP_A-1957920	rev/B	C/T	ttttcaacactgttag	aaagagagaagtgaaa	08/28/07	08/29/07	130	Genomic	unknown
ss80830675	HGSV\|Cor18507_SNV_20070510.chr7_49473728	fwd/T	A/G	tcctgttcctgatttttcacttctctcttt	ctaacagtgttgaaaatctccacacaggtt	11/26/07	11/26/07	130	Genomic	unknown
ss84665820	HGSV\|Cor19240_SNV_20070510.chr7_49473728	fwd/T	A/G	tcctgttcctgatttttcacttctctcttt	ctaacagtgttgaaaatctccacacaggtt	11/30/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 Ttttatatat caggcatcat gccatgtata atccttgggg atttttcact tatgctacct
 tgctaggatt catccacagt ttcatctgtc actacagtat actggtttgg attgtagaaa
 attattctat tgtgggaata cacagcaatt gattagtcta ctctccaggt gatttgcatt
 caatcatttc taggttttct cttctaaaca gggaagctat gaacattctt gcatgtcttc
 tgttggatat gtgtaattgt ttctctcaag tagttccaag tggaattgca aatgttagaa
 ggtatgtatt tcattttaga aaataatgcc gacctgtttc ccaaagaaac tgcaccaagc
 tcaatccagc agcaaaaatt gagagtacct atgtgtccac atcccttcca gaattgacat
 ttgcagattt tgtatgtgtg cctactgaac gagtataaaa tactaaatca tcctgttcct
 gatttttcac ttctctcttt
 R
 ctaacagtgt tgaaaatctc cacacaggtt tagtgggcac ctgtgttctt attttttaag
 acacctgttc aggcctctgc ctaactttcc attgattgCC CATGCTAACA ATGAGCCTGT
 CACCAGAGAA ATTGCCTCTG CATCACACCC TGAATGAGCA TGGCTATTTC CAGGACTCTA
 CTCTATGATT TCCCCCACTA CTCTTATCTA TGATGAGCTT TACTCTTTTG AGACTTTAGG
 GCAAACCCTC TTCATACTAA AGGAAACTTC AGGCAGGCAA AGAGAATGGG GAAATCAG

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4464911 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	670490	49583229	minus	T	alt_assembly_8	HuRef	HuRef	view	500
7	NT_030008.6	1459064	49667013	plus	A	ref_assembly	reference	reference	view	500
7	NT_079592.2	49689249	49739249	plus	A	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	500
7	NW_923273.1	5621395	49796745	plus	A	alt_assembly_1	Celera	Celera	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030008.5

dbSNP Blast Analysis
GenBank HTGS Finished:
AC092448.6 AC207178.4 NC_000007.12

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss19732107	HapMap-CEU	European	120	IG	0.383	0.550	0.067	0.100	0.658	0.342

	HapMap-HCB	Asian	88	IG	0.500	0.409	0.091	1.000	0.705	0.295

	HapMap-JPT	Asian	90	IG	0.511	0.400	0.089	1.000	0.711	0.289

	HapMap-YRI	Sub-Saharan African	114	IG	0.632	0.368		0.100	0.816	0.184

ss66346000	HapMap-CEU	European	118	GF	0.339	0.593	0.068		0.636	0.364

	HapMap-HCB	Asian	90	GF	0.511	0.400	0.089		0.711	0.289

	HapMap-JPT	Asian	90	GF	0.467	0.444	0.089		0.689	0.311

	HapMap-YRI	Sub-Saharan African	120	GF	0.633	0.367			0.817	0.183

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss19732107	264	132	111	14
ss66346000	263

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs4464911	270	132	111	14

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
373	ss19732107	A/A	CSHL-HAPMAP	HapMap-CEU	NA12264	CEPH1375.11	r23_ch7_CEU_perlegen:genotyping_1.0.0	3449337
373	ss66346000	C/T	CSHL-HAPMAP	HapMap-CEU	NA12264	CEPH1375.11	chr7-HapMap-CEU
457	ss19732107	G/G	CSHL-HAPMAP	HapMap-CEU	NA10839	CEPH1420.02	r23_ch7_CEU_perlegen:genotyping_1.0.0	3449337
457	ss66346000	C/T	CSHL-HAPMAP	HapMap-CEU	NA10839	CEPH1420.02	chr7-HapMap-CEU
618	ss19732107	A/A	CSHL-HAPMAP	HapMap-CEU	NA12872	CEPH1459.09	r23_ch7_CEU_perlegen:genotyping_1.0.0	3449337
618	ss66346000	C/T	CSHL-HAPMAP	HapMap-CEU	NA12872	CEPH1459.09	chr7-HapMap-CEU
5220	ss19732107	A/A	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	r23_ch7_JPT_perlegen:genotyping_1.0.0	3449337
5220	ss66346000	C/T	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	chr7-HapMap-JPT
5233	ss19732107	A/A	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	r23_ch7_JPT_perlegen:genotyping_1.0.0	3449337
5233	ss66346000	C/T	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	chr7-HapMap-JPT
5253	ss19732107	A/A	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	r23_ch7_YRI_perlegen:genotyping_1.0.0	3449337
5253	ss66346000	C/T	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	chr7-HapMap-YRI

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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .