Reference SNP(refSNP) Cluster Report: rs2146658

Reference SNP(refSNP) Cluster Report: rs2146658

refSNP ID: rs2146658
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/129
Map to Genome Build:	36.3

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

HGVS Names
NM_005427.1:c.430-972T>G
NT_004321.17:g.953393T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3074799 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2146658 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
ss3074799	TSC-CSHL\|TSC1166949	fwd/T	A/C	cctgctgggagtcctcatgctctctcccca	agggccatcaggaatgatccccagtctcag	06/07/01	10/25/06	96	Genomic	unknown
ss11412244	WI_SSAHASNP\|chr1.NT_004321.15_944388	rev/B	G/T	ctgagactggggatcattcctgatggccct	tggggagagagcatgaggactcccagcagg	07/03/03	10/10/03	116	Genomic	unknown
ss14819493	SC_SNP\|NT_004321.15_944388	rev/B	G/T	ctgagactggggatcattcctgatggccct	tggggagagagcatgaggactcccagcagg	11/12/03	11/22/03	119	Genomic	unknown
ss19148207	CSHL-HAPMAP\|CSHL-HuDD-200402.chr1.NT_004321.15_944388	rev/B	G/T	ctgagactggggatcattcctgatggccct	tggggagagagcatgaggactcccagcagg	02/20/04	03/04/04	120	Genomic	unknown
ss20533473	SSAHASNP\|WGSA-200403-chr1.chr1.NT_004321.15_944388	rev/B	G/T	ctgagactggggatcattcctgatggccct	tggggagagagcatgaggactcccagcagg	03/18/04	03/18/04	121	Genomic	unknown
ss23839183	PERLEGEN\|afd0701667	rev/B	G/T	ctgagactggggatcattcctgatggccct	tggggagagagcatgaggactcccagcagg	08/10/04	09/13/04	123	Genomic	unknown
ss75158684	ILLUMINA\|ILMN_Human_1M_rs2146658	fwd/T	A/C	cctgctgggagtcctcatgctctctcccca	agggccatcaggaatgatccccagtctcag	08/28/07	08/29/07	129	Genomic	unknown
ss77542602	HGSV\|Cor12156_SNV_20070510.chr1_3660770	rev/B	G/T	ctgagactggggatcattcctgatggccct	tggggagagagcatgaggactcccagcagg	10/09/07	10/13/07	129	Genomic	unknown

Fasta sequence (Legend)

 CAAGTCTGAG CAGCCGAGCT GTGTGGCTTG GTCTTGGCCA CTCTGGGGGC CCCTCTGGGC
 TCACAGCCCC AGTATCCCCA GCTTGGGACT CGAGGAGCTA ATAGGTCTGT CTGGAGCTGG
 CGTGGGCCCT GCTGCAGGAG GACTGGATGA CACCCTTCCT GAGCCAGCCC CTGCAGAGGC
 CTCCAGCTTC TTTGCCTCAC AGGGCCCGGC TGCCCATCTG AGGACCCAGG CCGGCTCTCA
 TGAGTTCTAA AAGTGACCCC GCTGAGGCCG CTGCAGGGGC GTCCACTCAC TTCCAAGCTG
 GCTGATTTCC CAAGCGTCTG GCTCCTGGTC ACCTGCTGGG AGTCCTCATG CTCTCTCCCC
 A
 M
 AGGGCCATCA GGAATGATCC CCAGTCTCAG GCTCAGAGAA TGACTTCTGC TGCCACCCCA
 TGCCCTCTGT GCCCCTCACC AGCCCCCGAT GACTCAGAAT CACAAGTCAC TGCAGCCGCA
 AGTGCCCTGG AGAATGTCCC ATCGCACTCC ACCGTGGAAC AGTTGGGGAA ACTGAGGTCA
 GAGACAGGGA GCTACTGGCA GAACCAGGGA AGCTGCAGGT GGAGTCTTCC CTTTGCCA

GeneView

GeneView via analysis of contig annotation: TP73 tumor protein p73

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_004321->NM_005427

function

HuRef

NW_001838618->NM_005427

function

Celera

NW_923572->NM_005427

function

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


reference	NT_004321->NM_005427->NP_005418	953393	forward	intron

HuRef	NW_001838618->NM_005427->NP_005418	205701	reverse	intron

Celera	NW_923572->NM_005427->NP_005418	460977	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2146658 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_923572.1	460977	2891651	minus	G	alt_assembly_1	Celera	Celera	view	361
1	NW_001838618.2	205701	2933441	plus	C	alt_assembly_8	HuRef	HuRef	view	361
1	NT_004321.17	953393	3627473	minus	T	ref_assembly	reference	reference	view	361

NCBI Resource Links

Submitter-Referenced
GenBank
NT_004321

dbSNP Blast Analysis
GenBank HTGS Finished:
AL136528.11

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss23839183	AFD_EUR_PANEL	European	48	IG	0.042	0.250	0.708	0.655	0.167	0.833

	AFD_AFR_PANEL	African American	46	IG	0.087	0.348	0.565	0.655	0.261	0.739

	AFD_CHN_PANEL	Asian	48	IG	0.250	0.583	0.167	0.403	0.542	0.458

ss3074799	HapMap-HCB	Asian	90	IG	0.289	0.578	0.133	0.251	0.578	0.422

	HapMap-JPT	Asian	88	IG	0.250	0.568	0.182	0.371	0.534	0.466

	HapMap-YRI	Sub-Saharan African	120	IG	0.050	0.383	0.567	0.752	0.242	0.758

	7		65	AF					0.292	0.708

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.478+/-0.102	251	200	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .