Reference SNP(refSNP) Cluster Report: rs709206

Reference SNP(refSNP) Cluster Report: rs709206

refSNP ID: rs709206
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_031215.2:c.*2252A>T
NT_011362.9:g.26016671T>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8376768 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs709206 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
ss1345286	TSC-CSHL\|TSC0193017	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	09/06/00	10/10/03	86	Genomic	95 %
ss1521837	LEE\|328147	rev/T	A/T	tgtggatgtcagtgtgcataagcaagtatc	gacctcagaatgtttgagttattttgtctt	09/13/00	10/10/03	86	cDNA	unknown
ss3239316	YUSUKE\|IMS-JST049401	rev/T	A/T	tgtggatgtcagtgtgcataagcaagtatc	gacctcagaatgtttgagttattttgtctt	09/05/01	10/10/03	100	Genomic	unknown
ss3401391	SC_JCM\|chr_20_62701423	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	09/24/01	10/10/03	100	Genomic	unknown
ss4393986	LEE\|ge328147	rev/T	A/T	tgtggatgtcagtgtgcataagcaagtatc	gacctcagaatgtttgagttattttgtctt	04/25/02	10/10/03	106	cDNA	unknown
ss4413344	LEE\|e328147	rev/T	A/T	tgtggatgtcagtgtgcataagcaagtatc	gacctcagaatgtttgagttattttgtctt	04/26/02	10/10/03	106	cDNA	unknown
ss8376768	SC_SNP\|NT_030871.1_1019548	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	04/17/03	05/16/04	114	Genomic	unknown
ss10956768	BCM_SSAHASNP\|chr20.NT_030871.1_1019548	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	06/30/03	10/10/03	116	Genomic	unknown
ss12484780	WI_SSAHASNP\|chr20.NT_030871.1_1019548	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	07/04/03	10/10/03	116	Genomic	unknown
ss16249226	CGAP-GAI\|1497271	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	11/18/03	11/22/03	120	cDNA	unknown
ss16891638	CSHL-HAPMAP\|CSHL-HuAA-200402.chr20.NT_030871.1_1019548	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	02/17/04	03/04/04	120	Genomic	unknown
ss21786933	SSAHASNP\|WGSA-200403-chr20.chr20.NT_030871.1_1019548	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	03/20/04	03/20/04	121	Genomic	unknown
ss24601700	PERLEGEN\|afd4245884	fwd/B	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	08/10/04	09/13/04	123	Genomic	unknown
ss78252551	HGSV\|Cor12878_SNV_20070510.chr20_60397170	fwd/	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	10/17/07	10/18/07	129	Genomic	unknown
ss85180916	HGSV\|Cor18517_SNV_20070510.chr20_60397170	fwd/	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	12/06/07	12/08/07	130	Genomic	unknown
ss91752794	BCMHGSC_JDW\|JWB-1463100	fwd/	A/T	aagacaaaataactcaaacattctgaggtc	gatacttgcttatgcacactgacatccaca	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATGATTCCAT TCTCCGATTG GCCAAGGCCG ATGGCATCGT CTCAAAGTAA GGTTGGGGGC
 TCACATTTGG GCAGAGTGAG TGGACTAGGA CTGCTCCAGA GGCGTGGTCT TAACGTTGTC
 CTTTTCCCCT GGTTCTAGGA ACTTTTGACT GGAGAGAATC ACAGATGTGG AATATTTGTC
 ATAAATAAAT AATGAAAACC TACCTGTGCA GGTTCATTCT GTGTCTGTAG GCCCAGGGTT
 GAGGTTTTGC TGTCAGTGGG TGACGGGTGG GGTAGGGTAC CCAGTTAGTT GAAAGGAGAC
 AAGCTGTGAA ACATATTGCA AAACTGAGGT TTAAAGGACA AATACATTAT CCATTTAAAA
 ACAGATATCT AAGACAAAAT AACTCAAACA TTCTGAGGTC
 W
 GATACTTGCT TATGCACACT GACATCCACA ACTGCTACCG GTGCGGAAGC AACGCCAGGC
 CTGGTTCTGT ATAGTCACAG CCGAGCTGAA CACCTTAGCT CCGACACCTG GATGTGTTCT
 AGAGAATGAC AGGCTGAGAC TGTAGTTTGG TTTAACTACT GGCTTTGTTG CAATAATCCT
 CGAATACCAC ACAGTGGCAG CTTTTGGCAT CATAAAAATG GGACATAACT GAAGGGAAGG
 CTTCACACAT CACAAAGACC GGGTTGGTTA ATGACTAAAT CTCACTACAT GAATACGCAA
 TCTTAAATTA CTGTGCTTAT CAGCCATTTC TCGCATTCAT GTGTAGGAAA AACCATGGAG
 ACGTGTCCCT GGAGGGCAGG TTGTAAACTG CAACAGTTAC

GeneView

GeneView via analysis of contig annotation: RPS21 ribosomal protein S21

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: CABLES2 Cdk5 and Abl enzyme substrate 2

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_011362->NM_001024

function

reference

NT_011362->NM_031215

function

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


reference	NT_011362->NM_001024->NP_001015	26016671	forward		3' near gene

reference	NT_011362->NM_031215->	26016671	reverse	3696	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs709206 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NW_927339.1	31202158	57699049	plus	A	alt_assembly_1	Celera	Celera	view	400
20	NW_001838669.2	115063	57740934	minus	T	alt_assembly_8	HuRef	HuRef	view	400
20	NT_011362.9	26016671	60397170	plus	T	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030871 AW274689 Hs.239942

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_031215.2	AL121832.56

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss24601700	AFD_EUR_PANEL	European	44	IG	0.136	0.591	0.273	0.343	0.432	0.568

	AFD_AFR_PANEL	African American	40	IG	0.900	0.100		1.000	0.950	0.050

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.333	0.583	0.655	0.250	0.750

ss3239316	JBIC-allele		1502	AF					0.075	0.925

ss8376768	CEPH		184	AF					0.450	0.550

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.499+/-0.023	71	50	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 .