Reference SNP(refSNP) Cluster Report: rs3204853

Reference SNP(refSNP) Cluster Report: rs3204853

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	105/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_016013.2:c.92G>T
NP_057097.2:p.Arg31Leu
NT_010194.16:g.12479723C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48413284 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3204853 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
ss4434669	LEE\|e1248587	fwd/B	G/T	cttctgccttgtatccatttttgggtattc	ctttgcagagtattccagtagtcttcagaa	04/26/02	10/10/03	105	cDNA	unknown
ss16242710	CGAP-GAI\|1482671	fwd/B	G/T	cttctgccttgtatccatttttgggtattc	ctttgcagagtattccagtagtcttcagaa	11/18/03	11/22/03	120	cDNA	unknown
ss17538163	CSHL-HAPMAP\|CSHL-HuCC-200402.chr15.NT_010194.16_12479723	rev/T	A/C	ttctgaagactactggaatactctgcaaag	gaatacccaaaaatggatacaaggcagaag	02/19/04	05/16/04	120	Genomic	unknown
ss48413284	APPLERA_GI\|hCV25742001	rev/T	A/C	ttctgaagactactggaatactctgcaaag	gaatacccaaaaatggatacaaggcagaag	09/28/05	11/03/06	126	Genomic	unknown
ss69174604	PERLEGEN\|PGP04767857	rev/T	A/C	ttctgaagactactggaatactctgcaaag	gaatacccaaaaatggatacaaggcagaag	01/30/07	01/30/07	127	Genomic	unknown
ss74811294	AFFY\|SNP_M-185242	fwd/B	G/T	cttctgccttgtatccatttttgggtattc	ctttgcagagtattccagtagtcttcagaa	08/09/07	08/09/07	128	Genomic	unknown
ss108764743	1000GENOMES\|CEU.trio.12.15.2008_3151459_chr15_39476458	rev/T	A/C	ttctgaagactactggaatactctgcaaag	gaatacccaaaaatggatacaaggcagaag	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 AAATAATAAT AATAATAATA GTAAACAAAT AAGTTAACAA ACTTCAAAAT ACCTGATTTC
 TGTTGAATTT GAAATTGTGA TGCATTCATT GCTATGCTGA TAATTCTTCA ATGTCTCTTC
 TGTTATAGGT AGAATTGGGC TATTTGCTGA AGCTTCTTGG TGGCCCTTGC TAGCCCAGGA
 AGAAACTTAC ATTTTGATTT TTTTGTACCA TGGCTTTGGT TCACAAATTG CTGCGTGGTA
 CTTATTTTCT CAGAAAATTC TCTAAGCCAA CTTCTGCCTT GTATCCATTT TTGGGTATTC
 K
 CTTTGCAGAG TATTCCAGTA GTCTTCAGAA ACCAGTGGCT TCTCCTGGCA AAGCCTCCTC
 ACAGAGGAAG ACTGAAGGGG ATTTGCAAGG AGATCACCAG AAAGAAGTTG CTTTGGATAT
 AACTTCTTCT GAGGAGAAGC CTGATGTTAG TTTCGATAAA GCAATTAGAG ATGAAGCAAT
 ATACCATTTT AGGCTTTTGA AGGATGAAAT TGTGGATCAT TGGAGAGGAC CGGAAGGCCA
 CCCTCTGCAT GAGGTCTTGC TGGAACAAGC CAAGGTTGTC TGGCAATTCC GGGGGAAAGA

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_010194 BF689899 Hs.106529

dbSNP Blast Analysis

UniGene Cluster ID
106529

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss17538163	CEPH		184	AF					0.900	0.100

ss48413284	HapMap-CEU	European	120	IG	0.667	0.317	0.017	0.479	0.825	0.175

	HapMap-HCB	Asian	90	IG	0.978	0.022			0.989	0.011

	HapMap-JPT	Asian	88	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

	AGI_ASP population	multiple	76	IG	0.737	0.263		0.371	0.868	0.132

ss69174604	HapMap-CEU	European	120	GF	1.000				1.000

	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	G/G	G/T	T/T
ss48413284	537

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs3204853	563

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
158	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12145	CEPH1334.11	r27_ch15_CEU_bcm:genotype_0002
171	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	r27_ch15_CEU_bcm:genotype_0002
175	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	r27_ch15_CEU_bcm:genotype_0002
184	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA07034	CEPH1341.11	r27_ch15_CEU_bcm:genotype_0002
186	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA06993	CEPH1341.13	r27_ch15_CEU_bcm:genotype_0002
187	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA06985	CEPH1341.14	r27_ch15_CEU_bcm:genotype_0002
199	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12056	CEPH1344.12	r27_ch15_CEU_bcm:genotype_0002
226	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch15_CEU_bcm:genotype_0002
239	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	r27_ch15_CEU_bcm:genotype_0002
263	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA11830	CEPH1350.11	r27_ch15_CEU_bcm:genotype_0002
349	ss48413284	A/A	CSHL-HAPMAP	HapMap-CEU	NA10861	CEPH1362.02	r27_ch15_CEU_bcm:genotype_0002
361	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA11993	CEPH1362.14	r27_ch15_CEU_bcm:genotype_0002
362	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	r27_ch15_CEU_bcm:genotype_0002
363	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA11995	CEPH1362.16	r27_ch15_CEU_bcm:genotype_0002
408	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12154	CEPH1408.10	r27_ch15_CEU_bcm:genotype_0002
409	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12236	CEPH1408.11	r27_ch15_CEU_bcm:genotype_0002
411	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12156	CEPH1408.13	r27_ch15_CEU_bcm:genotype_0002
465	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12004	CEPH1420.10	r27_ch15_CEU_bcm:genotype_0002
538	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	r27_ch15_CEU_bcm:genotype_0002
548	ss48413284	A/A	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch15_CEU_bcm:genotype_0002
610	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12864	CEPH1459.01	r27_ch15_CEU_bcm:genotype_0002
618	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12872	CEPH1459.09	r27_ch15_CEU_bcm:genotype_0002
619	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12873	CEPH1459.10	r27_ch15_CEU_bcm:genotype_0002
623	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12878	CEPH1463.02	r27_ch15_CEU_bcm:genotype_0002
637	ss48413284	A/C	CSHL-HAPMAP	HapMap-CEU	NA12892	CEPH1463.16	r27_ch15_CEU_bcm:genotype_0002
5154	ss48413284	A/C	CSHL-HAPMAP	HapMap-HCB	NA18562	CH18562	r27_ch15_CHB_bcm:genotype_0002

Genotype data submitted for	563	samples from	563	individuals	Individual with multiple genotypes submission:	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 .