Reference SNP(refSNP) Cluster Report: rs3087908

Reference SNP(refSNP) Cluster Report: rs3087908

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	102/130
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_023007.1:c.1382C>T
NP_075383.1:p.Ala461Val
NT_004559.13:g.4122257G>A
XM_001721461.1:c.144G>A
XM_001721656.1:c.144G>A
XM_001721832.1:c.144G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48401954 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3087908 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
ss4321796	CGAP-GAI\|251860	fwd/B	C/T	agcagctgagagaggctgttgatgctgctg	ggccccatagcacctgtcgtgaggatagaa	11/28/01	10/25/06	102	cDNA	unknown
ss24270785	PERLEGEN\|afd1194564	rev/T	A/G	ttctatcctcacgacaggtgctatggggcc	cagcagcatcaacagcctctctcagctgct	08/10/04	09/13/04	126	Genomic	unknown
ss48401954	APPLERA_GI\|hCV16006955	rev/T	A/G	ttctatcctcacgacaggtgctatggggcc	cagcagcatcaacagcctctctcagctgct	09/28/05	11/03/06	126	Genomic	unknown
ss68795341	PERLEGEN\|PGP01194564	rev/T	A/G	ttctatcctcacgacaggtgctatggggcc	cagcagcatcaacagcctctctcagctgct	01/30/07	03/31/08	127	Genomic	unknown
ss74864666	ILLUMINA\|ILMN_Human_1M_rs3087908	fwd/B	C/T	agcagctgagagaggctgttgatgctgctg	ggccccatagcacctgtcgtgaggatagaa	08/28/07	08/29/07	129	Genomic	unknown
ss86350878	CANCER-GENOME\|12863	rev/T	A/G	ttctatcctcacgacaggtgctatggggcc	cagcagcatcaacagcctctctcagctgct	01/25/08	01/25/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTCACTGGCC TCTTCCCTCT GCCCAGGTCA TCATGAGGTC CTGCTCGGGC ATCAACTTTG
 AAGAGTTTTA CCACTTCCTC AAGGTCATCG CTGAGAAGAG GCTCCTGGTC CTGAGGGAGG
 CAGCCGCTGA GGACGGTGCT GGGTTGGGTT TCGAACAGGC AGCCTTTGAT GTTGGGCGCA
 TCACAGAGGT GCTGGCCTCC TTGGTTGCGC ACCCCGACTT CCAGAGAGTG GACACCAGCG
 CGTTCTCACC ACAGCCCAAA GAGCTGCTGC AGCAGCTGAG AGAGGCTGTT GATGCTGCTG
 Y
 GGCCCCATAG CACCTGTCGT GAGGATAGAA GGACGGGTGG AAGAGAGGCA GCCTCCTGCT
 CCGGGGCCCT TCCAGAAATA AAGACCGCCC TCCCTGTGAC CTGGGGCCCA CCCCTGTCGA
 GGCTTGTGGC CTGGCTGTTC ATGGCCACTG CCTGGGTGCC TGTTTTCAGG TGAGGCCCAA
 TGAGGTCAGG GACCCAAGAT GGGATGTGGC CCTTCTGACC TGCAGCAGGC CTGCTGGGAG
 CTCGGAGATG GTGCCAGGAC CTGGCTCTTT TGGGGGCCCT GCCTCCTTAG GCCAGGACGC

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
dbSTS	GenBank
CGAP-C-25186	NC_000001.8

dbSNP Blast Analysis

UniGene Cluster ID
546427

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss24270785	AFD_EUR_PANEL	European	48	IG	0.625	0.333	0.042	1.000	0.792		0.208

	AFD_AFR_PANEL	African American	44	IG	0.636	0.318	0.045	1.000	0.795		0.205

	AFD_CHN_PANEL	Asian	46	IG	0.652	0.304	0.043	1.000	0.804		0.196

	CHMJ	Asian	74	IG					0.716	0.068	0.216

ss4321796	CEPH		184	AF					0.710		0.290

ss48401954	AGI_ASP population	multiple	74	IG	0.811	0.135	0.054	0.050	0.878		0.122

ss68795341	HapMap-CEU	European	120	GF	0.017	0.967	0.017		0.500		0.500

	HapMap-HCB	Asian	90	GF		0.956	0.044		0.478		0.522

	HapMap-JPT	Asian	90	GF	0.044	0.867	0.089		0.478		0.522

	HapMap-YRI	Sub-Saharan African	120	GF		1.000			0.500		0.500

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24270785	66
ss48401954	1241

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs3087908	1302

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
188	ss24270785	G/G	PERLEGEN	AFD_EUR_PANEL	NA10851		71_IND_CHR_1
188	ss48401954	N/N	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r27_ch1_CEU_illumina:human_1m_beadchip
203	ss24270785	G/G	PERLEGEN	AFD_EUR_PANEL	NA07348		71_IND_CHR_1
203	ss48401954	G/G	CSHL-HAPMAP	HapMap-CEU	NA07348	CEPH1345.02	r27_ch1_CEU_illumina:human_1m_beadchip
349	ss24270785	G/G	PERLEGEN	AFD_EUR_PANEL	NA10861		71_IND_CHR_1
349	ss48401954	G/G	CSHL-HAPMAP	HapMap-CEU	NA10861	CEPH1362.02	r27_ch1_CEU_illumina:human_1m_beadchip
399	ss24270785	G/G	PERLEGEN	AFD_EUR_PANEL	NA10830		71_IND_CHR_1
399	ss48401954	G/G	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	r27_ch1_CEU_illumina:human_1m_beadchip
400	ss24270785	G/G	PERLEGEN	AFD_EUR_PANEL	NA10831		71_IND_CHR_1
400	ss48401954	G/G	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	r27_ch1_CEU_illumina:human_1m_beadchip

Genotype data submitted for	1317	samples from	1302	individuals	Individual with multiple genotypes submission:	15

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

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .