Reference SNP(refSNP) Cluster Report: rs234740

Reference SNP(refSNP) Cluster Report: rs234740

refSNP ID: rs234740
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:	C/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_004571.3:c.*2737G>C
NT_030188.4:g.1447389G>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2273413 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs234740 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
ss303103	KWOK\|OVLP-000621-327815	rev/T	C/G	gacatagcctgagtttcctttaacctctct	caatgggtgcttttaactagcttctacatg	06/30/00	10/10/03	79	Genomic	97 %
ss506152	SC_JCM\|AC020600.2_134078	fwd/B	C/G	catgtagaagctagttaaaagcacccattg	agagaggttaaaggaaactcaggctatgtc	07/12/00	10/10/03	80	Genomic	unknown
ss2273413	TSC-CSHL\|TSC0687597	fwd/B	C/G	catgtagaagctagttaaaagcacccattg	agagaggttaaaggaaactcaggctatgtc	10/20/00	04/07/04	92	Genomic	95 %
ss4020916	PERLEGEN\|P00228457	rev/T	C/G	gacatagcctgagtttcctttaacctctct	caatgggtgcttttaactagcttctacatg	09/26/01	04/07/04	100	Genomic	unknown
ss23652821	PERLEGEN\|afd0101841	rev/T	C/G	gacatagcctgagtttcctttaacctctct	caatgggtgcttttaactagcttctacatg	08/10/04	09/13/04	123	Genomic	unknown
ss65733760	ILLUMINA\|Human1-rs234740	fwd/?	C/G	catgtagaagctagttaaaagcacccattg	agagaggttaaaggaaactcaggctatgtc	10/10/06	10/10/06	127	Genomic	unknown
ss66372115	AFFY\|SNP_A-2020257	fwd/B	C/G	ttaaaagcacccattg	agagaggttaaaggaa	10/29/06	08/14/07	127	Genomic	unknown
ss76099411	AFFY\|AFFY_6_1M_SNP_A-2020257	fwd/	C/G	ttaaaagcacccattg	agagaggttaaaggaa	08/28/07	08/30/07	129	Genomic	unknown
ss84320256	HGSV\|Cor18517_SNV_20070510.chr21_43326017	rev/	C/G	gacatagcctgagtttcctttaacctctct	caatgggtgcttttaactagcttctacatg	12/06/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 GGGTCACACT TTTACAGATT CTCTCCACTG TCCAAGGGCT GGAGAACAGG TGTTTTAAGG
 TGCCAACTGA CCTCAAACAT GCTGGGCAGT GATTTTGCAA ACTGAAACAG CTTGCCATGT
 AGAAGCTAGT TAAAAGCACC CATTG
 S
 AGAGAGGTTA AAGGAAACTC AGGCTATGTC CATAAGCACC CTTTCTCTAA GTGATCTTTA
 TCCTATTCCT CTGAATTTAG TAAGAATTTA GGAAAGTTGA AGAAAGTTTT CAGCTGGAGA
 GAATGCACAC TGTACCATTC AGCATGGGTG TTTAACTCTC AGGCCAGAGC TTCCCAGTGC
 CACCAAGGTT CAGGCAGTGC tctcttttta tagatggggg tctcactgtg ttgcccaaga
 tggagtgcag tggctattca caggtgcaag catagtgcac tgcagcctca aactcctggc
 acatgccatc ctctgcctca gactcccgag tagctggaac tagaggcacg ccctactgcg
 ccgggcAGGG GCAGCACTCT TAAATTCAAT CCACTGCTTA GTGAATGTGA TTTCTAGTGG
 GGGAAAGAAA CGGTGACCTA TACATGAGTC TACATTCTGT

GeneView

GeneView via analysis of contig annotation: PKNOX1 PBX/knotted 1 homeobox 1

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_030188->NM_004571

function

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


reference	NT_030188->NM_004571->	1447389	forward	4236	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs234740 maps exactly once on NCBI human chromosome 21

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
21	NW_927384.1	29090746	29605623	minus	G	alt_assembly_1	Celera	Celera	view	145
21	NW_001838715.2	181430	29871459	plus	G	alt_assembly_8	HuRef	HuRef	view	145
21	NT_030188.4	1447389	43326017	minus	G	ref_assembly	reference	reference	view	145

NCBI Resource Links

Submitter-Referenced
GenBank
NT_003545 AP001630

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_004571.3	AP001630.1 AP002085.1	AY142115.1 AY196965.1

UniGene Cluster ID
431043

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss2273413	CEPH		184	AF					0.790	0.210

	HapMap-CEU	European	118	IG	0.542	0.356	0.102	0.371	0.720	0.280

	HapMap-HCB	Asian	90	IG	0.778	0.222		0.403	0.889	0.111

	HapMap-JPT	Asian	88	IG	0.864	0.136		0.655	0.932	0.068

	HapMap-YRI	Sub-Saharan African	120	IG	0.633	0.333	0.033	0.752	0.800	0.200

ss23652821	AFD_EUR_PANEL	European	46	IG	0.696	0.261	0.043	0.752	0.826	0.174

	AFD_AFR_PANEL	African American	46	IG	0.565	0.391	0.043	0.752	0.761	0.239

	AFD_CHN_PANEL	Asian	48	IG	0.833	0.167		0.752	0.917	0.083

ss4020916	NCBI\|NIHPDR		19	AF					0.842	0.158

ss66372115	HapMap-CEU	European	118	GF	0.542	0.356	0.102		0.720	0.280

	HapMap-HCB	Asian	90	GF	0.778	0.222			0.889	0.111

	HapMap-JPT	Asian	90	GF	0.867	0.133			0.933	0.067

	HapMap-YRI	Sub-Saharan African	120	GF	0.633	0.333	0.033		0.800	0.200

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.287+/-0.247	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

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .