Reference SNP(refSNP) Cluster Report: rs2070955

Reference SNP(refSNP) Cluster Report: rs2070955

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/130
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
NM_000147.3:c.4C>T
NP_000138.2:p.Arg2Trp
NT_004610.18:g.7019115G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss28477321 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2070955 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
ss2984397	YUSUKE\|IMS-JST006077	fwd/B	C/T	agtgggccgcgtcgctgaggggtagcgatg	gggctccggggatgaggtcgcggccggcgg	05/24/01	10/10/03	96	Genomic	unknown
ss3186055	HGBASE\|SNP000571639	fwd/B	C/T	gccgcgtcgctgaggggtagcgatg	gggctccggggatgaggtcgcggcc	07/09/01	10/10/03	102	Genomic	unknown
ss3508276	SC_JCM\|AL590609.4_1305	rev/T	A/G	ccgcccgccgcgacctcatccccggagccc	catcgctacccctcggcgacgcggcccact	09/24/01	10/10/03	100	Genomic	unknown
ss4227976	SC_JCM\|AL590609.12_1305	rev/T	A/G	ccgcccgccgcgacctcatccccggagccc	catcgctacccctcggcgacgcggcccact	10/15/01	10/10/03	101	Genomic	unknown
ss4369443	SC_JCM\|AL590728.10_112243	rev/T	A/G	ccgccggccgcgacctcatccccggagccc	catcgctacccctcagcgacgcggcccact	02/19/02	10/10/03	103	Genomic	unknown
ss12993121	SC_SNP\|NT_004391.15_535120	rev/T	A/G	ccgccggccgcgacctcatccccggagccc	catcgctacccctcagcgacgcggcccact	10/22/03	10/31/03	123	Genomic	unknown
ss13457380	WI_SSAHASNP\|chr1.NT_079488.1_1305	rev/T	A/G	ccgcccgccgcgacctcatccccggagccc	catcgctacccctcggcgacgcggcccact	10/31/03	11/10/03	123	Genomic	unknown
ss13540528	BCM_SSAHASNP\|chr1.NT_079488.1_1305	rev/T	A/G	ccgcccgccgcgacctcatccccggagccc	catcgctacccctcggcgacgcggcccact	11/05/03	11/22/03	123	Genomic	unknown
ss20524928	SSAHASNP\|WGSA-200403-chr1.chr1.NT_079488.1_1305	rev/T	A/G	ccgcccgccgcgacctcatccccggagccc	catcgctacccctcggcgacgcggcccact	03/18/04	03/18/04	123	Genomic	unknown
ss23856311	PERLEGEN\|afd4475380	rev/T	A/G	ccgccggccgcgacctcatccccggagccc	catcgctacccctcagcgacgcggcccact	08/10/04	09/13/04	123	Genomic	unknown
ss28477321	KYUGEN\|QH06419	fwd/B	C/T	agtgggccgcgtcgcygaggggtagcgatg	gggctccggggatgaggtcgcggcsggcgg	07/29/04	11/02/06	126	Genomic	unknown
ss77528214	HGSV\|Cor12156_SNV_20070510.chr1_23940079	rev/T	A/G	ccgccggccgcgacctcatccccggagccc	catcgctacccctcagcgacgcggcccact	10/09/07	10/13/07	129	Genomic	unknown
ss83121442	HGSV\|Cor18555_SNV_20070510.chr1_23940079	rev/T	A/G	ccgccggccgcgacctcatccccggagccc	catcgctacccctcagcgacgcggcccact	11/27/07	12/04/07	130	Genomic	unknown
ss86239234	CORNELL\|hCV15868073	rev/B	C/T	ccgccggccgcgacctcatccccggagccc	catcgctacccctcagcgacgcggcccact	01/21/08	01/21/08	129	Genomic	unknown

Fasta sequence (Legend)

 GTCTTGCTCA CCTCCACGAT TTAACCTCGC AGTTAAGTCC CTTTTCAAGG TTTTTATTCG
 TCCTTCAGCG AAGCGCTGTC AACGCCTCCC TGCGTCTTTC CCTTCTTGAG CACCAGAGGG
 CGCTCCTCCG ACCCGAGGAG GAAGCGACTC KGGCCAACCT GTCCAGGTTG TCCCACCCCT
 TTTTCCKTCC GGGCCAATCG TTAGTCAGAG TGGGCGGAGC CGCCCGCGGG CACCTGCGCG
 TTAAGAGTGG GCCGCGTCGC YGAGGGGTAG CGATG
 Y
 GGGCTCCGGG GATGAGGTCG CGGCSGGCGG GTCCCGCGCT GTTGCTGCTG CTGCTCTTCC
 TCGGAGCGGC CGAGTCGGTG CGTCGGGCCC AGCCTCCGCG CCGCTACACC CCAGACTGGC
 CGAGCCTGGA TTCTCGGCCG CTGCCGGCCT GGTTCGACGA AGCCAAGTTC GGGGTGTTCA
 TCCACTGGAA C

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_079488 AL590609 AL590728

dbSNP Blast Analysis

UniGene Cluster ID
370858

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23856311	AFD_EUR_PANEL	European	48	IG	0.792	0.167	0.042	0.251	0.875	0.125

	AFD_AFR_PANEL	African American	44	IG	0.727	0.273		0.479	0.864	0.136

	AFD_CHN_PANEL	Asian	48	IG	0.583	0.417		0.200	0.792	0.208

ss28477321	CP		156	AF					0.860	0.140

	JPK3		200	AF					0.790	0.210

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.265+/-0.250	71	50	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	YES	YES

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .