Reference SNP(refSNP) Cluster Report: rs5951079

Reference SNP(refSNP) Cluster Report: rs5951079

refSNP ID: rs5951079
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	114/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001005332.1:c.-37+9438A>G
NT_011638.12:g.1531478A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss19808669 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5951079 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
ss8236039	SC_SNP\|NT_038056.1_108919	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	04/16/03	10/10/03	114	Genomic	unknown
ss8496415	SC_SNP\|NT_011638.11_1519112	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	05/23/03	10/10/03	117	Genomic	unknown
ss19808669	CSHL-HAPMAP\|CSHL-HuDD-200402.chrX.NT_011638.12_1531478	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	02/20/04	10/30/04	120	Genomic	unknown
ss20385532	CSHL-HAPMAP\|CSHL-HuFF-200402.chrX.NT_011638.12_1531478	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	02/21/04	03/04/04	120	Genomic	unknown
ss43566324	ABI\|hCV2116714	rev/B	C/T	actaagacatgctataatatggataaactt	gaaaacactatgctaactggaagaagtgag	07/18/05	07/18/05	126	Genomic	unknown
ss76645195	AFFY\|AFFY_6_1M_SNP_A-8506472	fwd/T	A/G	ttagcatagtgttttc	aagtttatccatatta	08/28/07	08/30/07	129	Genomic	unknown
ss77358555	HGSV\|Cor12156_SNV_20070510.chrX_51388687	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	10/09/07	10/12/07	129	Genomic	unknown
ss82756208	HGSV\|Cor18956_SNV_20070510.chrX_51388687	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	11/30/07	12/03/07	130	Genomic	unknown
ss83029286	HGSV\|Cor19240_SNV_20070510.chrX_51388687	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	11/30/07	12/04/07	130	Genomic	unknown
ss94284328	BCMHGSC_JDW\|JWB-2679239	fwd/T	A/G	ctcacttcttccagttagcatagtgttttc	aagtttatccatattatagcatgtcttagt	02/26/08	03/06/08	129	Genomic	unknown

Fasta sequence (Legend)

 TTGACAAAAA AAAGCTGTGA GTGGGACCAG AGAGCAAGTG GTCATTGGTC ATTTAGACGA
 TGTAAAGTAG CTGACTGGAT ATGCCATTTA GCCTTGAGCT TGAAAGTACC TAAAATAATG
 GGCAATTTAG AGGTTACTCT GTGGTCTAGT AAAGCTAAGG AAAAGGGGCA AATGGAAAGG
 AATAGTTTTA TAAATGGTGT ccccattctc ccagcccatg gcaaccacta atatactctc
 tgtctctctg aatttcccta ttctgaacat ttcatataac tagagtcttg aaatatgtgg
 ccttctgtgt ctcacttctt ccagttagca tagtgttttc
 R
 aagtttatcc atattatagc atgtcttagt atttccattc cttttcatgg ctgaaagata
 ttccattgta tgagtatacc accttttatg tattcattca tcagattgta gatggacaga
 tgagttgttt ctactttttg gctattatga ataatgctgc tgtgaacttc tggtatacgt
 ttttgtgcaa acatatgttc ttctcatttc tctggggtat atgcctagga gtgaaattga
 tagtaactct atacttaact ctttgaagaa ctgccaaact cttttccaaa atggctctac
 cacttaaatt cccaccagga atgtataagg ttccaatttc tccacatcct tgctaacact
 tgttgttttc cttttttttt ttttttaaat tacaaccatc ttagtgagta tATATAATAA
 AGAATCTCAC ttaattttta aaatataata tttaaCCGCT GACATCTTTT TTTTTTTTTT
 TTTTTGAGGC AGACTTTCAC

GeneView

GeneView via analysis of contig annotation: MAGED1 melanoma antigen family D, 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_011638->NM_001005332

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_011638->NM_001005332->NP_001005332	1531478	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs5951079 maps exactly once on NCBI human chromosome X

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
X	NW_001842365.2	266622	48992479	minus	T	alt_assembly_8	HuRef	HuRef	view	340
X	NT_011638.12	1531478	51572391	plus	A	ref_assembly	reference	reference	view	340
X	NW_927705.1	666226	56175261	minus	T	alt_assembly_1	Celera	Celera	view	340

NCBI Resource Links

Submitter-Referenced
GenBank
NT_038056

dbSNP Blast Analysis
GenBank HTGS Finished:
AL929101.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss19808669	HapMap-CEU	European	120	IG	0.267	0.150	0.583	0.100	0.342	0.658

	HapMap-HCB	Asian	90	IG	0.044	0.067	0.889	0.050	0.078	0.922

	HapMap-JPT	Asian	88	IG	0.045	0.114	0.841	0.752	0.102	0.898

	HapMap-YRI	Sub-Saharan African	120	IG	0.517	0.283	0.200	0.200	0.658	0.342

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.439+/-0.164	270	210	0	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 .