Reference SNP(refSNP) Cluster Report: rs2295994

Reference SNP(refSNP) Cluster Report: rs2295994

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/130
Map to Genome Build:	36.3

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

HGVS Names
NM_023007.1:c.195T>G
NM_053052.2:c.-193A>C
NP_075383.1:p.Asp65Glu
NT_004559.13:g.4125072A>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss41352977 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2295994 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
ss3239950	YUSUKE\|IMS-JST050035	fwd/B	G/T	cgacagccacttccgaggcctgggggtcga	gtccccggcgtcggccaggctccgggccgg	09/05/01	10/10/03	100	Genomic	unknown
ss16261138	CGAP-GAI\|1522555	fwd/B	G/T	cgacagccacttccgaggcctgggggtcga	gtccccggcgtcggccaggctccgggccgg	11/18/03	11/22/03	120	cDNA	unknown
ss16265321	CGAP-GAI\|1531035	fwd/B	G/T	cgacagccacttccgaggcctgggggtcga	gtccccggcgtcggccaggctccgggccgg	11/18/03	11/22/03	120	cDNA	unknown
ss17327358	CSHL-HAPMAP\|CSHL-HuCC-200402.chr1.NT_004559.11_4099112	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	02/19/04	03/04/04	120	Genomic	unknown
ss24270827	PERLEGEN\|afd3990425	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	08/10/04	09/13/04	123	Genomic	unknown
ss41352977	ABI\|hCV1688934	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	07/16/05	11/03/06	126	Genomic	unknown
ss48401958	APPLERA_GI\|hCV1688934	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	09/28/05	11/03/06	126	Genomic	unknown
ss79747435	HGSV\|Cor18507_SNV_20070510.chr1_224229653	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	11/23/07	11/23/07	130	Genomic	unknown
ss86342320	CANCER-GENOME\|17087	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	01/25/08	01/25/08	129	Genomic	unknown
ss87997107	BCMHGSC_JDW\|JWB-0196172	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	02/26/08	02/27/08	129	Genomic	unknown
ss111884399	1000GENOMES\|NA19240_2008_12_16_237997_chr1_225989541	rev/T	A/C	ccggcccggagcctggccgacgccggggac	tcgacccccaggcctcggaagtggctgtcg	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 ACCAACACCG TCGCTCACCT GAGGGACGCC AGACGAGTCC CAGAGCCGAC CGCGGCGCCT
 CGGCCGCTCG GCGCCTGCGC AGTGAAGACC GCGGCGAGCC GCGCGCATGC GTGCAGGCCC
 GGAGCCCCAG GCGCTGGTGG GGCAGAAACG CGGCGCCCTG CGTCTTCTGG TTCCGAGGCT
 GGTCCTCACC GTTTCCGCTC CGGCGGAAGT GAGGAGGAGG GTCCTTCGAC CCGTGCTGAG
 CTGGATGGAC CGCGAGACGC GCGCCCTCGC CGACAGCCAC TTCCGAGGCC TGGGGGTCGA
 K
 GTCCCCGGCG TCGGCCAGGC TCCGGGCCGG GTAGCCTTCG TCTCGGAGCC GGGCGCCTTC
 TCCTACGCCG ACTTTGTGCG GGGCTTCTTG CTGCCCAACC TGCCCTGCGT GTTTTCCAGC
 GCCTTCACGC AGGGCTGGGG CAGCCGGCGG CGCTGGGTGA CGCCCGCGGG GAGGCCCGAC
 TTCGACCACC TGCTACGGAC CTACGGTGGG GCGGCGGCCG CAGACCCCGG GCGGGGAGGA
 AAGGCCGGCG GGACCCAGGC CCGGGAGGCC CCCGCCTAGA GAGGGGCACC AGGGAGGGTG

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_004559 BM473197 BU184048

dbSNP Blast Analysis

UniGene Cluster ID
325081

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss24270827	AFD_EUR_PANEL	European	44	IG	0.318	0.500	0.182	1.000	0.568	0.432

	AFD_AFR_PANEL	African American	42	IG	0.238	0.333	0.429	0.200	0.405	0.595

	AFD_CHN_PANEL	Asian	46	IG	0.043	0.522	0.435	0.273	0.304	0.696

ss3239950	JBIC-allele		1502	AF					0.340	0.660

ss41352977	HapMap-CEU	European	120	IG	0.200	0.433	0.367	0.403	0.417	0.583

	HapMap-HCB	Asian	90	IG	0.133	0.556	0.311	0.343	0.411	0.589

	HapMap-JPT	Asian	86	IG	0.140	0.419	0.442	0.655	0.349	0.651

	HapMap-YRI	Sub-Saharan African	120	IG	0.150	0.483	0.367	1.000	0.392	0.608

ss48401958	AGI_ASP population	multiple	18	IG	0.111	0.111	0.778	0.100	0.167	0.833

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.478+/-0.104	603	481	15	0

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 .