Reference SNP(refSNP) Cluster Report: rs153179

Reference SNP(refSNP) Cluster Report: rs153179

refSNP ID: rs153179
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1626297 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs153179 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
ss221699	KWOK\|OVLP-000621-44562	rev/B	C/T	gaacacaccctggcagcacttgcagcgtga	gaggttgagggaatgtgtcgctgaggtcgt	06/30/00	10/10/03	79	Genomic	98 %
ss327593	KWOK\|OVLP-000621-43782	rev/B	C/T	gaacacaccctggcagcacttgcagcgtga	gaggttgagggaatgtgtcgctgaggtcgt	06/30/00	10/10/03	79	Genomic	99 %
ss925360	KWOK\|OVLP-000804-265667	fwd/T	A/G	acgacctcagcgacacattccctcaacctc	tcacgctgcaagtgctgccagggtgtgttc	09/01/00	10/10/03	86	Genomic	99 %
ss990970	KWOK\|OVLP-000804-276035	fwd/T	A/G	acgacctcagcgacacattccctcaacctc	tcacgctgcaagtgctgccagggtgtgttc	09/02/00	10/10/03	86	Genomic	98 %
ss1626297	KWOK\|OVLP-000925-366180	fwd/T	A/G	acgacctcagcgacacattccctcaacctc	tcacgctgcaagtgctgccagggtgtgttc	10/04/00	03/31/08	87	Genomic	98 %
ss2462102	SC_JCM\|AC007615.4_180567	fwd/T	A/G	acgacctcagcgacacattccctcaacctc	tcacgctgcaagtgctgccagggtgtgttc	11/03/00	10/10/03	92	Genomic	unknown
ss6607361	WI_SSAHASNP\|NT_010604.11_5510050	fwd/T	A/G	acgacctcagcgacacattccctcaacctc	tcacgctgcaagtgctgccagggtgtgttc	02/12/03	10/10/03	111	Genomic	unknown
ss14257483	BCM_SSAHASNP\|chr16.NT_024812.10_631439	fwd/T	A/G	acgacctcagcgacacattccctcaacctc	tcacgctgcaagtgctgccagggtgtgttc	11/05/03	11/22/03	119	Genomic	unknown
ss76612942	AFFY\|AFFY_6_1M_SNP_A-8474227	rev/B	C/T	agcacttgcagcgtga	gaggttgagggaatgt	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 CGTTCCCGTT TCAGGGGGGA AGCTGCAGAG TTCTGGAGCT GTGAGTAGCA CCGCTGTCAC
 CGCAAAGCAG AACCCCCAGT GATTAGGGAC GCTCCACGGA CTTCACGGCT GCGCGGCCGG
 CATCACGGGC TGCTGTTGCT CCAGCGTGTT GGGACGTGCG AGAGGCATTT ACGACCTCAG
 CGACACATTC CCTCAACCTC
 R
 TCACGCTGCA AGTGCTGCCA GGGTGTGTTC AGGGGACACT CCCTCTCGGG CTGGCTTGTG
 CGGGGACACG TGCGTGCACA CAGACACGGA CTCACATAAA TGCAATCCAC ATGCACTCAC
 AATAGGCTCT TATGCACAGA CCCTCACACT CATGTGAACA CACTCATGCA CACGCAAGAC
 TTACATATTC ACACTCACAC CCGTGGGCAC ACCCAGACAT GGatacacac tcatacaggc
 acacacgtat ccagacaccc acgcacagac acactcacac ccacgggcac acctagacat
 ggatacacac acaggtagtc acaagcactc acatatccag acacccatgc gcacactcac
 actcacaggc acacccagac atggatacac aggcacacac atattgggac acccacgcat
 agacacattc acacacgggc acacccagac tgatgcacac gaacacagac atgcacTAGT
 ATAGCCAGAC ACCCAGGCAC ACT

GeneView

GeneView via analysis of contig annotation: RUNDC2B RUN domain containing 2B

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

HuRef

NW_001838231->XM_001714307

function

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


HuRef	NW_001838231->XM_001714307->XP_001714359	124348	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs153179 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838231.2	124348	27098430	minus	C	alt_assembly_8	HuRef	HuRef	view	200
16	NW_926251.1	99750	27386649	minus	T	alt_assembly_1	Celera	Celera	view	200
16	NT_010393.15	20543274	29137696	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024812 AC009093.5 AC009130 AC009130.6

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
ss1626297	HapMap-CEU	European	120	IG	0.200	0.500	0.300		0.450	0.550

	HapMap-HCB	Asian	90	IG	0.200	0.511	0.289		0.456	0.544

	HapMap-JPT	Asian	90	IG	0.178	0.578	0.244		0.467	0.533

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.496+/-0.043	180	150	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .