Reference SNP(refSNP) Cluster Report: rs7683365

Reference SNP(refSNP) Cluster Report: rs7683365

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/130
Map to Genome Build:	36.3

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

HGVS Names
NG_007483.1:g.24901C>T
NM_002100.3:c.143C>T
NP_002091.2:p.Thr48Met

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss42378530 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7683365 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
ss11664893	WI_SSAHASNP\|chr4.NT_016606.15_6440261	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	07/03/03	10/10/03	116	Genomic	unknown
ss14603585	WI_SSAHASNP\|chr4.NT_016606.16_6468652	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	11/05/03	11/22/03	119	Genomic	unknown
ss17011157	CSHL-HAPMAP\|CSHL-HuAA-200402.chr4.NT_016606.16_6468652	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	02/17/04	03/04/04	120	Genomic	unknown
ss42378530	ABI\|hCV34183121	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	07/17/05	11/03/06	126	Genomic	unknown
ss68913689	PERLEGEN\|PGP13384986	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	01/30/07	03/31/08	127	Genomic	unknown
ss77695187	HGSV\|Cor12156_SNV_20070510.chr4_145278201	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	10/09/07	10/14/07	129	Genomic	unknown
ss78594347	HGSV\|Cor12878_SNV_20070510.chr4_145278201	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	10/17/07	10/20/07	129	Genomic	unknown
ss92814782	BCMHGSC_JDW\|JWB-1867126	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	02/26/08	03/03/08	129	Genomic	unknown
ss99015886	HUMANGENOME_JCVI\|1103654574711	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	04/02/08	04/02/08	130	Genomic	unknown
ss108423874	1000GENOMES\|CEU.trio.12.15.2008_1107456_chr4_145140046	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	12/15/08	12/15/08	130	Genomic	unknown
ss117223357	ILLUMINA-UK\|NA18507_000193698_NCBI36.1_chr4_145140046	fwd/T	A/G	ggtacagtgaaacgatggacaagttgtccc	tttctcctataaagcaaaatttcaatgtaa	01/18/09	01/18/09	130	Genomic	99 %

Fasta sequence (Legend)

 AGTGATTAGC CAGGCTTGGC CTCCCAAAAT TATAGGGATT ATAGGCATGA GCCACGGCCC
 CTGGCCCCCA AAATGTTTTT AAAAATAAGA AATGCCTATT TTAATTTTAA AAAGAGAATA
 TTTTCTTTGT CTTTACAATT TCGTGTGAAT AAAGTTAACA ACATATGCTC TTCTGTTTTA
 AGATAGACAC ATTTTCTTAG GCATTTGAAA CAAGCAATGG ATAGTTTAAA ATGGAATGAC
 TTTTATTCTT TGTCAAATAT TAACATACCT GGTACAGTGA AACGATGGAC AAGTTGTCCC
 R
 TTTCTCCTAT AAAGCAAAAT TTCAATGTAA GTCCAAATAA GAAAGACATG TGCAAAGAAA
 AAAATCATTT TGGAATCAAA CTGTTCTGCG GGTTTCCTTT TCTTAATCAT ATTTTGAGAG
 TTGTTGGTCA ACTTTCAACA TCTAGCTAGT AACATTTATG AGGTAATGTG TCAGTCTTAC
 CATTAGTAAT TTCAGTATCT ACTTTTAATG ACCCAACACG TATTCATGGA TGAGAAATAA
 GCAAATTGTC TCATAACTGA GGGGAAAGGA ATGAGAAAGT ATTGGAAGAA TCACTTATTG

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_016606 ABBA01070007

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss42378530	HapMap-CEU	European	96	IG	0.167	0.604	0.229	0.150	0.469	0.531

ss68913689	HapMap-CEU	European	120	GF	0.117	0.500	0.383		0.367	0.633

	HapMap-HCB	Asian	90	GF		0.178	0.822		0.089	0.911

	HapMap-JPT	Asian	88	GF	0.023	0.114	0.864		0.080	0.920

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.467	0.517		0.250	0.750

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss42378530	168	9	38	20
ss99015886	1		1

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs7683365	175	9	39	20

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
169	ss42378530	A/G	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	r27_ch4_CEU_bcm:genotype_0002
186	ss42378530	A/A	CSHL-HAPMAP	HapMap-CEU	NA06993	CEPH1341.13	r27_ch4_CEU_bcm:genotype_0002
255	ss42378530	A/G	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r27_ch4_CEU_bcm:genotype_0002
262	ss42378530	A/G	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r27_ch4_CEU_bcm:genotype_0002
456	ss42378530	A/A	CSHL-HAPMAP	HapMap-CEU	NA10838	CEPH1420.01	r27_ch4_CEU_bcm:genotype_0002
536	ss42378530	G/G	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch4_CEU_bcm:genotype_0002

Genotype data submitted for	175	samples from	175	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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .