Reference SNP(refSNP) Cluster Report: rs302949

Reference SNP(refSNP) Cluster Report: rs302949

refSNP ID: rs302949
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:	A
Clinical Association:	unknown

HGVS Names
NM_005339.3:c.64-835C>T
NT_016297.15:g.6886848C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2029331 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs302949 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
ss390647	KWOK\|OVLP-000621-217850	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	06/30/00	10/10/03	79	Genomic	99 %
ss393036	KWOK\|OVLP-000621-223421	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	06/30/00	10/10/03	85	Genomic	99 %
ss557863	SC_JCM\|AC027207.3_44110	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	07/12/00	10/10/03	80	Genomic	unknown
ss982519	KWOK\|OVLP-000804-588727	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	09/01/00	10/10/03	86	Genomic	99 %
ss983166	KWOK\|OVLP-000804-591484	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	09/01/00	10/10/03	86	Genomic	99 %
ss2029331	KWOK\|OVLP-000925-671038	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	10/06/00	04/07/04	87	Genomic	99 %
ss2029625	KWOK\|OVLP-000925-676381	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	10/06/00	10/10/03	87	Genomic	99 %
ss6886404	WI_SSAHASNP\|NT_037627.1_783761	rev/B	C/T	gtggagagcccatttgctggcaggcactta	gaatgttaatgtgagtcccactggatggtt	02/12/03	10/10/03	111	Genomic	unknown
ss11675948	WI_SSAHASNP\|chr4.NT_016297.14_6886848	rev/B	C/T	gtggagagcccatttgctggcaggcactta	gaatgttaatgtgagtcccactggatggtt	07/03/03	10/10/03	116	Genomic	unknown
ss14596272	WI_SSAHASNP\|chr4.NT_016297.15_6886848	rev/B	C/T	gtggagagcccatttgctggcaggcactta	gaatgttaatgtgagtcccactggatggtt	11/05/03	11/22/03	119	Genomic	unknown
ss22095300	SSAHASNP\|WGSA-200403-chr4.chr4.NT_016297.15_6886848	rev/B	C/T	gtggagagcccatttgctggcaggcactta	gaatgttaatgtgagtcccactggatggtt	03/20/04	03/20/04	121	Genomic	unknown
ss24653448	PERLEGEN\|afd3462083	rev/B	C/T	gtggagagcccatttgctggcaggcactta	gaatgttaatgtgagtcccactggatggtt	08/10/04	09/13/04	123	Genomic	unknown
ss44477770	ABI\|hCV911255	rev/B	C/T	gtggagagcccatttgctggcaggcactta	gaatgttaatgtgagtcccactggatggtt	07/19/05	07/19/05	126	Genomic	unknown
ss75161961	ILLUMINA\|ILMN_Human_1M_rs302949	fwd/T	A/G	aaccatccagtgggactcacattaacattc	taagtgcctgccagcaaatgggctctccac	08/28/07	08/29/07	129	Genomic	unknown
ss81036910	HGSV\|Cor18555_SNV_20070510.chr4_39560771	rev/B	C/T	gtggagagcccatttgctggcaggcactta	gaatgttaatgtgagtcccactggatggtt	11/27/07	11/27/07	130	Genomic	unknown

Fasta sequence (Legend)

 AACGGCAACT ACCTACTTCA AAAAACCAGA TTTCTACTTT AAATTTATCT ACATTGACTT
 ATTTTGCACT TTAAACTACT CCAAGTACTT TCCTATCTAT AGCATTACTG AGTCTCTTAA
 CCTTATGACA GTCCATTCTC AGAGCCATGA TAACCTTAAA TGATTCAGAA AACCATCCAG
 TGGGACTCAC ATTAACATTC
 R
 TAAGTGCCTG CCAGCAAATG GGCTCTCCAC TTATATTCTC AAACCTATGT TAAAAATACA
 GTAAATCCTC TCGATTTTTT AAACCAAAAT CCCTAAAGAA CAGGTTACAT CTTCCttttt
 ttgagacgga gtcttgctct tgctgcccag gctggagtgc gatggcacga tctcggctca
 ctgcaacctc cacctcctgg gttcaagtga ctctcctgct tcagcctcct gagtagctgg
 gattacaggc acccactacc atgctcagct aatttttgtt atttttagtc gagacggggt
 ttcgccacgt tggccaggct tgtctcgaac tcctgacctc gcgatacgcc cgccttggcc
 tcccaaagtg ctgggattat agacgtgagg caccgtgccc ggccTATATC TTCATTTTTT
 TTGGTTAGAA TTCCATATTG TTACCTGATT GACACAACAT ATCTACTCTT ATGTTTTTTG
 CTTTTAGACT GACTTTCTTA AAC

GeneView

GeneView via analysis of contig annotation: UBE2K ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)

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_016297->NM_005339

function

HuRef

NW_001838902->NM_005339

function

Celera

NW_922073->NM_005339

function

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


reference	NT_016297->NM_005339->NP_005330	6886848	forward	intron

HuRef	NW_001838902->NM_005339->NP_005330	983455	forward	intron

Celera	NW_922073->NM_005339->NP_005330	30303145	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs302949 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838902.1	983455	39063236	minus	T	alt_assembly_8	HuRef	HuRef	view	200
4	NT_016297.15	6886848	39414600	minus	C	ref_assembly	reference	reference	view	200
4	NW_922073.1	30303145	40176403	minus	T	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016297 AC023006 AC023328.2 AC027207.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC108471.3 NC_000004.10	AC023006.3 AC027207.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss2029331	HapMap-CEU	European	120	IG	0.583	0.350	0.067	0.752	0.758	0.242

	HapMap-HCB	Asian	90	IG	0.800	0.178	0.022	0.527	0.889	0.111

	HapMap-JPT	Asian	88	IG	0.818	0.159	0.023	0.403	0.898	0.102

	HapMap-YRI	Sub-Saharan African	120	IG	0.933	0.067		1.000	0.967	0.033

ss24653448	AFD_EUR_PANEL	European	48	IG	0.625	0.375		0.273	0.812	0.188

	AFD_AFR_PANEL	African American	46	IG	0.739	0.261		0.479	0.870	0.130

	AFD_CHN_PANEL	Asian	48	IG	0.917	0.083		1.000	0.958	0.042

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.216+/-0.248	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .