Reference SNP(refSNP) Cluster Report: rs296827

Reference SNP(refSNP) Cluster Report: rs296827

refSNP ID: rs296827
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:	G/T
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_016282.2:c.564-117C>A
NT_008413.17:g.4703213G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1931158 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs296827 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
ss383637	KWOK\|OVLP-000621-199436	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	06/30/00	10/10/03	79	Genomic	99 %
ss623633	SC_JCM\|AL353142.3_5684	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	07/12/00	10/10/03	80	Genomic	unknown
ss709987	SC_JCM\|AL353151.5_12252	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	07/27/00	10/10/03	85	Genomic	unknown
ss1188346	KWOK\|OVLP-000804-622745	rev/T	A/C	caagtgcctttctctcctgattacacaaat	tatacttaccaagactcctatatctacaat	09/02/00	10/10/03	86	Genomic	99 %
ss1931158	KWOK\|OVLP-000925-703981	rev/T	A/C	caagtgcctttctctcctgattacacaaat	tatacttaccaagactcctatatctacaat	10/06/00	10/25/06	87	Genomic	99 %
ss1965491	KWOK\|OVLP-000925-698945	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	10/06/00	10/10/03	87	Genomic	97 %
ss2608774	SC_JCM\|AL353151.9_118706	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	11/03/00	10/10/03	89	Genomic	unknown
ss4207701	SC_JCM\|AL353151.16_11854	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	10/15/01	10/10/03	101	Genomic	unknown
ss12927122	SC_SNP\|NT_008413.15_4703213	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	10/21/03	10/31/03	119	Genomic	unknown
ss15958336	SC_SNP\|NT_008413.16_4703213	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	11/17/03	11/22/03	120	Genomic	unknown
ss75063984	ILLUMINA\|ILMN_Human_1M_rs296827	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	08/28/07	08/29/07	129	Genomic	unknown
ss76420374	AFFY\|AFFY_6_1M_SNP_A-8281276	fwd/B	G/T	agtcttggtaagtata	atttgtgtaatcagga	08/28/07	08/30/07	129	Genomic	unknown
ss78427611	HGSV\|Cor12878_SNV_20070510.chr9_4703213	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	10/17/07	10/19/07	129	Genomic	unknown
ss80114720	HGSV\|Cor18507_SNV_20070510.chr9_4703213	fwd/B	G/T	attgtagatataggagtcttggtaagtata	atttgtgtaatcaggagagaaaggcacttg	11/23/07	11/24/07	130	Genomic	unknown

Fasta sequence (Legend)

 ACTTTAGTTT GTAGGAAAGC ATATACATAG GGCCAAATCT TGTTGGTTTC TGTTCCGGAG
 AATGTTTCCA GCACCCCTTT TTTCCTAAAG ATGAAACAAA AACAAAACAA ACACACACAG
 GTCTGAGTCT TCCTAATAAG CTCTTTCAAA GCCTTTCTGT AAATAATGAT ATTGTAGATA
 TAGGAGTCTT GGTAAGTATA
 K
 ATTTGTGTAA TCAGGAGAGA AAGGCACTTG GCTGGGCATT GGAAAATGTA CATTTTGGTT
 TCAGTTGTGC TCTCTGGCTT ACAAAAATGG GTGCTTAAAA AAATAACAGC ACCTATCATT
 TATTTTattt attgaacatg cactgtgtgt caaaggctgt gctacatgct ttacatatta
 tagtttgttt aatcctTTCC AAAGCTCAAA TTTTCTTATT TTACTAATAA AATCATCCCT
 TTGTAATGTA ACTTAGCCCA AATCACCAAG TTGGTAGTAC ATTTCCAAAC AGGACC

GeneView

GeneView via analysis of contig annotation: AK3 adenylate kinase 3

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_008413->NM_016282

function

HuRef

NW_001839149->NM_016282

function

Celera

NW_924062->NM_016282

function

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


reference	NT_008413->NM_016282->NP_057366	4703213	reverse	intron

HuRef	NW_001839149->NM_016282->NP_057366	31199666	forward	intron

Celera	NW_924062->NM_016282->NP_057366	4520240	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs296827 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_924062.1	4520240	4635721	plus	G	alt_assembly_1	Celera	Celera	view	200
9	NW_001839149.2	31199666	4668555	minus	C	alt_assembly_8	HuRef	HuRef	view	200
9	NT_008413.17	4703213	4703213	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008413 AL136231 AL353142 AL353151 AL353151.8 AL353151.9

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL136231.12 NC_000009.10	AL353142.6

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss1931158	HapMap-CEU	European	112	IG	0.857	0.125	0.018	0.251	0.920	0.080

	HapMap-HCB	Asian	84	IG	0.976	0.024		1.000	0.988	0.012

	HapMap-JPT	Asian	76	IG	0.895	0.105			0.947	0.053

	HapMap-YRI	Sub-Saharan African	108	IG	0.630	0.333	0.037	1.000	0.796	0.204

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.172+/-0.237	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 .