Reference SNP(refSNP) Cluster Report: rs4920104

Reference SNP(refSNP) Cluster Report: rs4920104

refSNP ID: rs4920104
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001001895.1:c.1625-125G>A
NM_018961.2:c.1739-125G>A
NT_030188.4:g.858960G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44247172 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4920104 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
ss6801385	WI_SSAHASNP\|NT_030188.2_613845	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	02/12/03	10/25/06	111	Genomic	unknown
ss17703967	CSHL-HAPMAP\|CSHL-HuCC-200402.chr21.NT_030188.3_613845	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	02/19/04	03/04/04	120	Genomic	unknown
ss19484431	CSHL-HAPMAP\|CSHL-HuDD-200402.chr21.NT_030188.3_613845	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	02/20/04	03/04/04	120	Genomic	unknown
ss21811027	SSAHASNP\|WGSA-200403-chr21.chr21.NT_030188.3_613845	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	03/20/04	03/20/04	121	Genomic	unknown
ss44247172	ABI\|hCV1724101	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	07/18/05	11/03/06	126	Genomic	unknown
ss66685419	ILLUMINA\|HumanHap300v1.1_rs4920104	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	11/09/06	11/09/06	127	Genomic	unknown
ss67398798	ILLUMINA\|HumanHap550v1.1_rs4920104	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	11/14/06	11/14/06	127	Genomic	unknown
ss67769071	ILLUMINA\|HumanHap650Yv1.0_rs4920104	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	11/14/06	11/14/06	127	Genomic	unknown
ss69255437	PERLEGEN\|PGP00100894	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	01/30/07	03/31/08	127	Genomic	unknown
ss70836107	ILLUMINA\|HumanHap550v3.0__rs4920104	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	04/20/07	03/31/08	130	Genomic	unknown
ss71419365	ILLUMINA\|HumanHap650Yv3.0_rs4920104	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	04/23/07	04/23/07	127	Genomic	unknown
ss75587980	ILLUMINA\|ILMN_Human_1M_rs4920104	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	08/28/07	08/29/07	129	Genomic	unknown
ss76480936	AFFY\|AFFY_6_1M_SNP_A-8342054	rev/B	C/T	agcctggcgagacccc	gggctagaagtagtgt	08/28/07	08/30/07	129	Genomic	unknown
ss79202553	ILLUMINA\|HumanHap300v2.0_rs4920104	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	04/18/07	11/18/07	130	Genomic	unknown
ss84398690	KRIBB_YJKIM\|KHS701819	fwd/T	A/G	agcggttaccagccacactacttctagccc	ggggtctcgccaggcttcggggcactctga	12/04/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCCACTCGGC CTGTGGTCTC CAGGTGTTCT TATCTAAAGC AGGAGTCGTA GCAGGCTCGT
 GTGACAAAAT AACCGGCTGA CCTTTCTAAA GTGAATCAGG TCTGGCTTGG GCGTCAGCCA
 CCGCTACATC CCAGTCTGTG GCTGACGGGG CCCAGGCAGC CAGCGACCAC AGGGGGTGGC
 TCAGCTCACT TCCTAGGCCT CCCTGAGGCT GGTGGGCAGC TGCTGCGTGC AGAGGAATCC
 ATGAGCGAGG GTGGGACGCA GGCATCACTG AGCGGTTACC AGCCACACTA CTTCTAGCCC
 R
 GGGGTCTCGC CAGGCTTCGG GGCACTCTGA GATAGCTCTG CCCCCCACCA CTTTGGGGAC
 CCCAGTCTAA TAAAAGGTGC TCTCTGGGGC TGCTTTGACC TGGAGGTGTT CTTGTTTTCC
 ACAGCGGGTG TCATCCTAAT TGTGAGTCAC GGCTCCACTC TGGACTCCTG CACGCGGCCA
 CTGCTCGGGC TGCCGCCCCG GGAATGTGGG GATTTTGCCC AACTCGTGAG AAAGGTACGC
 GCCCACTCTT GGCTCTTTGG GCCACAAAAT CAAGCATCCC GAAGACACAG GTTTATCTCA

GeneView

GeneView via analysis of contig annotation: UBASH3A ubiquitin associated and SH3 domain containing, A

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_030188->NM_001001895

function

reference

NT_030188->NM_018961

function

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


reference	NT_030188->NM_001001895->NP_001001895	858960	forward	intron

reference	NT_030188->NM_018961->NP_061834	858960	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4920104 maps exactly once on NCBI human chromosome 21

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
21	NW_927384.1	28498613	29013490	plus	A	alt_assembly_1	Celera	Celera	view	300
21	NW_001838715.2	771036	29281853	minus	T	alt_assembly_8	HuRef	HuRef	view	300
21	NT_030188.4	858960	42737588	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030188

dbSNP Blast Analysis
GenBank HTGS Finished:
AP001624.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss44247172	HapMap-CEU	European	118	IG	0.305	0.542	0.153	0.403	0.576	0.424

	HapMap-HCB	Asian	88	IG	0.273	0.568	0.159	0.317	0.557	0.443

	HapMap-JPT	Asian	88	IG	0.159	0.545	0.295	0.479	0.432	0.568

	HapMap-YRI	Sub-Saharan African	120	IG	0.067	0.517	0.417	0.200	0.325	0.675

ss69255437	HapMap-CEU	European	120	GF	0.300	0.550	0.150		0.575	0.425

	HapMap-HCB	Asian	90	GF	0.267	0.578	0.156		0.556	0.444

	HapMap-JPT	Asian	90	GF	0.156	0.533	0.311		0.422	0.578

	HapMap-YRI	Sub-Saharan African	120	GF	0.067	0.517	0.417		0.325	0.675

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.498+/-0.032	270	210	270	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .