Reference SNP(refSNP) Cluster Report: rs2270004

Reference SNP(refSNP) Cluster Report: rs2270004

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

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

HGVS Names
NM_152268.2:c.704A>G
NP_689481.2:p.Asn235Ser
NT_032977.8:g.25196050T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44032667 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2270004 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
ss3204284	YUSUKE\|IMS-JST024368	fwd/T	A/G	tggtgtgtgatgcctactgcagcctgttca	caagctagggctgccatttgtcaaggtcca	09/05/01	10/10/03	100	Genomic	unknown
ss44032667	ABI\|hCV3155029	rev/B	C/T	tggaccttgacaaatggcagccctagcttg	tgaacaggctgcagtaggcatcacacacca	07/18/05	11/03/06	126	Genomic	unknown
ss48408052	APPLERA_GI\|hCV3155029	fwd/T	A/G	tggtgtgtgatgcctactgcagcctgttca	caagctagggctgccatttgtcaaggtcca	09/28/05	11/03/06	126	Genomic	unknown
ss65726393	ILLUMINA\|Human1-rs2270004	fwd/T	A/G	tggtgtgtgatgcctactgcagcctgttca	caagctagggctgccatttgtcaaggtcca	10/10/06	10/10/06	127	Genomic	unknown
ss68766272	PERLEGEN\|PGP04525014	rev/B	C/T	tggaccttgacaaatggcagccctagcttg	tgaacaggctgcagtaggcatcacacacca	01/30/07	08/14/07	127	Genomic	unknown
ss78039214	HGSV\|Cor12878_SNV_20070510.chr1_54936152	rev/B	C/T	tggaccttgacaaatggcagccctagcttg	tgaacaggctgcagtaggcatcacacacca	10/17/07	10/17/07	129	Genomic	unknown
ss99208320	HUMANGENOME_JCVI\|1103675096565	rev/B	C/T	tggaccttgacaaatggcagccctagcttg	tgaacaggctgcagtaggcatcacacacca	04/03/08	04/03/08	130	Genomic	unknown
ss108201899	1000GENOMES\|CEU.trio.12.15.2008_65240_chr1_54996719	rev/B	C/T	tggaccttgacaaatggcagccctagcttg	tgaacaggctgcagtaggcatcacacacca	12/15/08	12/15/08	130	Genomic	unknown

Fasta sequence (Legend)

 ACTTGATGGG CAAAGAGCTG CTAAGACTTA GAGACAGGCA TGGCAAGGAA TACTGCTTAG
 GACCAACTCA CGAGGAAGCC ATTACGGCCT TAATTGCCTC CCAGAAGAAA CTGTCCTACA
 AGCAGCTTCC CTTCCTGCTG TACCAAGTGA CAAGGAAGTT TCGGGATGAG CCCAGGCCCC
 GCTTTGGTCT TCTCCGTGGC CGAGAGTTTT ACATGAAGGA TATGTACACC TTTGACTCCT
 CCCCAGAGGC TGCCCAGCAG ACCTACAGCC TGGTGTGTGA TGCCTACTGC AGCCTGTTCA
 R
 CAAGCTAGGG CTGCCATTTG TCAAGGTCCA GGCCGATGTG GGCACCATCG GGGGCACAGT
 GTCTCATGAG TTCCAGCTCC CAGTGGATAT TGGAGAGGAC CGGCTTGCCA TCTGTCCCCG
 CTGCAGCTTC TCAGCCAACA TGGAGACACT AGACTTGTCA CAAATGAACT GCCCTGCTTG
 CCAGGGCCCA TTGACTAAAA CCAAAGGCAT TGAGGTGGGG CACACATTTT ACCTGGGTAC
 CAAGTACTCA TCCATTTTCA ATGCCCAGTT TACCAATGTC TGTGGCAAAC CAACCCTGGC

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
NC_000001.8 ABBA01074707

dbSNP Blast Analysis

UniGene Cluster ID
380169

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss3204284	JBIC-allele		1468	AF					0.788	0.212

ss44032667	HapMap-CEU	European	120	IG	0.667	0.267	0.067	0.200	0.800	0.200

	HapMap-HCB	Asian	90	IG	0.822	0.133	0.044	0.050	0.889	0.111

	HapMap-JPT	Asian	88	IG	0.773	0.205	0.023	0.752	0.875	0.125

	HapMap-YRI	Sub-Saharan African	120	IG	0.717	0.233	0.050	0.251	0.833	0.167

	AoD_African_American		90	AF					0.850	0.150

	AoD_Caucasian		92	AF					0.890	0.110

	AoD_Chinese		90	AF					0.930	0.070

	AoD_Japanese		90	AF					0.770	0.230

ss48408052	AGI_ASP population	multiple	76	IG	0.789	0.132	0.079	0.005	0.855	0.145

ss68766272	HapMap-CEU	European	120	GF	0.633	0.300	0.067		0.783	0.217

	HapMap-HCB	Asian	90	GF	0.822	0.133	0.044		0.889	0.111

	HapMap-JPT	Asian	90	GF	0.733	0.244	0.022		0.856	0.144

	HapMap-YRI	Sub-Saharan African	120	GF	0.717	0.233	0.050		0.833	0.167

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss44032667	521
ss48408052	39	30	5	3
ss68766272	266
ss99208320	1

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs2270004	565	30	5	3

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
200	ss44032667	T/T	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r27_ch1_CEU_bcm:genotype_0002	220291
200	ss68766272	C/T	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	chr1-HapMap-CEU
254	ss44032667	T/T	CSHL-HAPMAP	HapMap-CEU	NA10856	CEPH1350.01	r27_ch1_CEU_bcm:genotype_0002	220291
254	ss68766272	C/T	CSHL-HAPMAP	HapMap-CEU	NA10856	CEPH1350.01	chr1-HapMap-CEU
548	ss44032667	T/T	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch1_CEU_bcm:genotype_0002	220291
548	ss68766272	C/T	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	chr1-HapMap-CEU
5193	ss44032667	T/T	CSHL-HAPMAP	HapMap-JPT	NA18942	JA18942	r27_ch1_JPT_bcm:genotype_0002	220291
5193	ss68766272	C/T	CSHL-HAPMAP	HapMap-JPT	NA18942	JA18942	chr1-HapMap-JPT

Genotype data submitted for	565	samples from	565	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 .