Reference SNP(refSNP) Cluster Report: rs26938

Reference SNP(refSNP) Cluster Report: rs26938

refSNP ID: rs26938
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
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_198859.2:c.*1605T>G
NT_022517.17:g.64023162A>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44373834 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs26938 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
ss39506	KWOK\|OVLP-78463	fwd/B	G/T	ggattgtggcagttgaaataatccatcgga	gacccacctgtagtgagatgtactgtcgat	04/28/00	10/10/03	76	Genomic	99 %
ss40040	KWOK\|OVLP-87005	fwd/B	G/T	ggattgtggcagttgaaataatccatcgga	gacccacctgtagtgagatgtactgtcgat	04/28/00	10/10/03	76	Genomic	99 %
ss415378	KWOK\|OVLP-000621-283625	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	06/30/00	10/10/03	79	Genomic	99 %
ss1136632	KWOK\|OVLP-000804-390521	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	09/02/00	10/10/03	86	Genomic	99 %
ss1138651	KWOK\|OVLP-000804-398476	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	09/02/00	10/10/03	86	Genomic	99 %
ss1141306	KWOK\|OVLP-000804-413224	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	09/02/00	10/10/03	86	Genomic	99 %
ss1141914	KWOK\|OVLP-000804-416144	fwd/B	G/T	ggattgtggcagttgaaataatccatcgga	gacccacctgtagtgagatgtactgtcgat	09/02/00	10/10/03	86	Genomic	99 %
ss1785156	KWOK\|OVLP-000925-431373	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	10/05/00	10/10/03	87	Genomic	99 %
ss1787134	KWOK\|OVLP-000925-453277	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	10/05/00	10/10/03	87	Genomic	99 %
ss1787635	KWOK\|OVLP-000925-462531	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	10/05/00	10/10/03	87	Genomic	99 %
ss1787794	KWOK\|OVLP-000925-467064	fwd/B	G/T	ggattgtggcagttgaaataatccatcgga	gacccacctgtagtgagatgtactgtcgat	10/05/00	10/10/03	87	Genomic	99 %
ss3669826	SC_JCM\|AC021023.8_117717	fwd/B	G/T	ggattgtggcagttgaaataatccatcgga	gacccacctgtagtgagatgtactgtcgat	09/24/01	10/10/03	100	Genomic	unknown
ss6457349	WI_SSAHASNP\|NT_005999.13_3087216	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	02/12/03	10/10/03	111	Genomic	unknown
ss10052885	BCM_SSAHASNP\|chr3.NT_005999.15_13020983	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	06/27/03	10/10/03	116	Genomic	unknown
ss11566988	WI_SSAHASNP\|chr3.NT_005999.15_13020983	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	07/03/03	10/10/03	116	Genomic	unknown
ss16951919	CSHL-HAPMAP\|CSHL-HuAA-200402.chr3.NT_022517.16_64005460	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	02/17/04	03/04/04	120	Genomic	unknown
ss19519456	CSHL-HAPMAP\|CSHL-HuDD-200402.chr3.NT_022517.16_64005460	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	02/20/04	03/04/04	120	Genomic	unknown
ss21968864	SSAHASNP\|WGSA-200403-chr3.chr3.NT_022517.16_64005460	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	03/20/04	03/20/04	121	Genomic	unknown
ss23217605	PERLEGEN\|afd2372572	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	08/10/04	09/13/04	123	Genomic	unknown
ss44373834	ABI\|hCV618581	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	07/18/05	11/03/06	126	Genomic	unknown
ss66193925	AFFY\|SNP_A-2261922	fwd/B	G/T	gaaataatccatcgga	gacccacctgtagtga	10/27/06	08/14/07	127	Genomic	unknown
ss75167748	ILLUMINA\|ILMN_Human_1M_rs26938	fwd/B	G/T	ggattgtggcagttgaaataatccatcgga	gacccacctgtagtgagatgtactgtcgat	08/28/07	08/29/07	129	Genomic	unknown
ss76273495	AFFY\|AFFY_6_1M_SNP_A-2261922	fwd/B	G/T	gaaataatccatcgga	gacccacctgtagtga	08/28/07	08/30/07	129	Genomic	unknown
ss81303738	HGSV\|Cor18507_SNV_20070510.chr3_64058162	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	11/26/07	11/29/07	130	Genomic	unknown
ss82431141	HGSV\|Cor18956_SNV_20070510.chr3_64058162	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	11/30/07	12/02/07	130	Genomic	unknown
ss82627765	HGSV\|Cor19240_SNV_20070510.chr3_64058162	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	11/30/07	12/03/07	130	Genomic	unknown
ss92116182	BCMHGSC_JDW\|JWB-1603315	rev/T	A/C	atcgacagtacatctcactacaggtgggtc	tccgatggattatttcaactgccacaatcc	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 ACCAGCTTAG TAACCAGAGT ATCTGGATTA CCCAGGAAGG TTGAGCTGCT GAGATTTCAG
 TGGTGCAATG TCTTTAAAAA AACAGGCTTT GTTGGGAGGG TATTTCCATT TTGAACTTTG
 AGGACTGTTG GTCAGAAAAT GGGCTCAAAA GTGAGTTTGC TTAATGAAGA CATTTAACGG
 TTGTGCTGTT TATAGTAAAA TAAAACTCCC TACCTTGCTT CAGTTAAAAA TGAAGCACTT
 GGTTTCTTCC ATCCTCCTCC TCCCCTTAAT GGATTGTGGC AGTTGAAATA ATCCATCGGA
 K
 GACCCACCTG TAGTGAGATG TACTGTCGAT GTAGTGCCCG GTGTATCTCA GTGGCCATCT
 GCCATGGTGA GGTGAGCGTG ATCTCTTTTC AGTATAGTAG TTAACATTTT CTAGTATTTT
 TTATGGAGAG AATGTCAAAA GTGGCATTTC AGACCCCGTC CCAGATGGGT CTGAGGAAAG
 GAAGGCTGTA AAGGACATGG TAATGGCACT CCATTCGGGA TGTATTAAAA TAATTTGCTT
 TTCAGGTATT AATATGACAT TTGTCATTGT CACTGATTTT TTTAAAAAAG CAATGCACAT

GeneView

GeneView via analysis of contig annotation: PRICKLE2 prickle homolog 2 (Drosophila)

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_022517->NM_198859

function

HuRef

NW_001838877->NM_198859

function

Celera

NW_921651->NM_198859

function

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


reference	NT_022517->NM_198859->	64023162	reverse	4726	3' UTR

HuRef	NW_001838877->NM_198859->	2087416	forward	4726	3' UTR

Celera	NW_921651->NM_198859->	64099891	reverse	4726	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs26938 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NT_022517.17	64023162	64058162	minus	A	ref_assembly	reference	reference	view	300
3	NW_921651.1	64099891	64099891	minus	C	alt_assembly_1	Celera	Celera	view	300
3	NW_001838877.2	2087416	64180246	plus	G	alt_assembly_8	HuRef	HuRef	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022517 AC007944 AC011312 AC018656 AC018656.10 AC021023.7 AC021023.8 AC021874 AC021874.17 AC021874.18

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank mRNA:
NM_198859.2	BX537915.1

UniGene Cluster ID
148105

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss23217605	AFD_EUR_PANEL	European	48	IG	1.000				1.000

	AFD_AFR_PANEL	African American	46	IG	0.783	0.130	0.087	0.020	0.848	0.152

	AFD_CHN_PANEL	Asian	48	IG	0.958	0.042		1.000	0.979	0.021

ss44373834	HapMap-CEU	European	120	IG	1.000				1.000

	HapMap-HCB	Asian	90	IG	0.933	0.067		1.000	0.967	0.033

	HapMap-JPT	Asian	90	IG	0.978	0.022		1.000	0.989	0.011

	HapMap-YRI	Sub-Saharan African	120	IG	0.617	0.283	0.100		0.758	0.242

ss66193925	HapMap-CEU	European	118	GF	1.000				1.000

	HapMap-HCB	Asian	90	GF	0.933	0.067			0.967	0.033

	HapMap-JPT	Asian	90	GF	0.978	0.022			0.989	0.011

	HapMap-YRI	Sub-Saharan African	120	GF	0.617	0.283	0.100		0.758	0.242

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.140+/-0.224	332	260	269	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

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Revised: May 25, 2006 1:38 PM .