Reference SNP(refSNP) Cluster Report: rs4905265

Reference SNP(refSNP) Cluster Report: rs4905265

refSNP ID: rs4905265
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NT_026437.11:g.76428907C>T
XM_001134296.1:c.-45-37G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss6779187 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4905265 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
ss6779187	WI_SSAHASNP\|NT_026437.9_58739505	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	02/12/03	10/25/06	111	Genomic	unknown
ss67396392	ILLUMINA\|HumanHap550v1.1_rs4905265	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	11/14/06	11/14/06	127	Genomic	unknown
ss67767708	ILLUMINA\|HumanHap650Yv1.0_rs4905265	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	11/14/06	11/14/06	127	Genomic	unknown
ss68240019	ILLUMINA\|HumanHap250Sv1.0_rs4905265	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	12/06/06	12/07/06	127	Genomic	unknown
ss69167264	PERLEGEN\|PGP08001024	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	01/30/07	03/31/08	127	Genomic	unknown
ss70834891	ILLUMINA\|HumanHap550v3.0__rs4905265	rev/T	A/G	ggtggtggcggggaatgggtctcatgtgtt	gaaaatttattccataaaatgattctcatt	04/20/07	03/31/08	130	Genomic	unknown
ss71417989	ILLUMINA\|HumanHap650Yv3.0_rs4905265	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	04/23/07	04/23/07	127	Genomic	unknown
ss74933413	ILLUMINA\|ILMN_Human_1M_rs4905265	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	08/28/07	08/29/07	129	Genomic	unknown
ss76533909	AFFY\|AFFY_6_1M_SNP_A-8394861	fwd/B	C/T	tatggaataaattttc	aacacatgagacccat	08/28/07	08/30/07	129	Genomic	unknown
ss84393917	KRIBB_YJKIM\|KHS700690	fwd/B	C/T	aatgagaatcattttatggaataaattttc	aacacatgagacccattccccgccaccacc	12/04/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 CACAGGCCCC CAGTGGGTCT GCCCAGAGCG AGCAGCCCGC CTTGGCCTTG TCTCAGCAGA
 CACTGCCTAG CAGCCTCAGG GTGTGGCCCG AGGCAGACAG CCTGATTGTC ATCACTCATC
 AGCAGGCGAC AAGTCGCTTA ACCTCCAAAC CTCAGCTTCC TTGTCTATAA AATGAGAATC
 ATTTTATGGA ATAAATTTTC
 Y
 AACACATGAG ACCCATTCCC CGCCACCACC AGCAAAAAAT GTACCCAAAA CATTCCATCA
 CCAGTACTAT AGCACTGAGG CTGAGCCTCG AAGCCATCAA ATCATGAATT GGCAACTGCA
 GGTCACACCA TTTCCCCATC TCTTCAATAT TCCGTTTTCT GCATGAACAA AATTGTATGT
 TTTCCAATCA TTTTCAATGC

GeneView

GeneView via analysis of contig annotation: LOC730118 hypothetical LOC730118

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_026437->XM_001134296

function

HuRef

NW_001838113->XM_001718787

function

Celera

NW_925561->XM_001724459

function

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


reference	NT_026437->XM_001134296->XP_001134296	76428907	reverse	intron

HuRef	NW_001838113->XM_001718787->XP_001718839	298734	forward	intron

Celera	NW_925561->XM_001724459->XP_001724511	42239875	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4905265 maps exactly once on NCBI human chromosome 14

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
14	NW_925561.1	42239875	75485345	plus	C	alt_assembly_1	Celera	Celera	view	200
14	NW_001838113.2	298734	75609808	minus	G	alt_assembly_8	HuRef	HuRef	view	200
14	NT_026437.11	76428907	94498907	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000014.7

dbSNP Blast Analysis
GenBank HTGS Finished:
AL390254.6 NC_000014.7

UniGene Cluster ID
448541

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss6779187	HapMap-CEU	European	120	IG	0.850	0.117	0.033	0.025	0.908	0.092

	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

ss69167264	HapMap-CEU	European	120	GF	0.850	0.133	0.017		0.917	0.083

	HapMap-HCB	Asian	90	GF	1.000				1.000

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss6779187	268	256	11	1
ss69167264	268	256	11	1

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs4905265	270	256	11	1

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
409	ss6779187	T/T	CSHL-HAPMAP	HapMap-CEU	NA12236	CEPH1408.11	r23_ch14_CEU_perlegen:genotyping_1.0.0	4971408
409	ss69167264	C/T	CSHL-HAPMAP	HapMap-CEU	NA12236	CEPH1408.11	chr14-HapMap-CEU
565	ss6779187	T/T	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	r23_ch14_CEU_perlegen:genotyping_1.0.0	4971408
565	ss69167264	C/T	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	chr14-HapMap-CEU

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	270

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 .