Reference SNP(refSNP) Cluster Report: rs729269

Reference SNP(refSNP) Cluster Report: rs729269

refSNP ID: rs729269
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_001039350.1:c.136-7367G>A
NT_034885.3:g.141476G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44819001 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs729269 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
ss73990	TSC-CSHL\|TSC0029949	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	09/06/00	04/07/04	86	Genomic	95 %
ss4993657	YUSUKE\|IMS-JST166643	rev/T	A/G	atagtcacacatgaggaccacaaagcagat	ttatcattctcctgggccttatgtacatct	08/12/02	10/10/03	108	Genomic	unknown
ss11878343	WI_SSAHASNP\|chr7.NT_034885.2_141476	rev/T	A/G	atagtcacacatgaggaccacaaagcagat	ttatcattctcctgggccttatgtacatct	07/04/03	04/07/04	116	Genomic	unknown
ss17174406	CSHL-HAPMAP\|CSHL-HuAA-200402.chr7.NT_034885.3_141476	rev/T	A/G	atagtcacacatgaggaccacaaagcagat	ttatcattctcctgggccttatgtacatct	02/17/04	03/04/04	120	Genomic	unknown
ss22522913	SSAHASNP\|WGSA-200403-chr7.chr7.NT_034885.3_141476	rev/T	A/G	atagtcacacatgaggaccacaaagcagat	ttatcattctcctgggccttatgtacatct	03/21/04	03/21/04	121	Genomic	unknown
ss24463435	PERLEGEN\|afd4326981	rev/T	A/G	atagtcacacatgaggaccacaaagcagat	ttatcattctcctgggccttatgtacatct	08/10/04	09/13/04	123	Genomic	unknown
ss44819001	ABI\|hCV1933025	rev/T	A/G	atagtcacacatgaggaccacaaagcagat	ttatcattctcctgggccttatgtacatct	07/19/05	11/03/06	126	Genomic	unknown
ss66593970	ILLUMINA\|HumanHap300v1.1_rs729269	fwd/T	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	11/09/06	11/09/06	127	Genomic	unknown
ss67565526	ILLUMINA\|HumanHap550v1.1_rs729269	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	11/14/06	11/14/06	127	Genomic	unknown
ss67944342	ILLUMINA\|HumanHap650Yv1.0_rs729269	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	11/14/06	11/15/06	127	Genomic	unknown
ss68368333	CSHL-HAPMAP\|wicgr:assay:hapmap_7q-rs729269:1	rev/T	A/G	atagtcacacatgaggaccacaaagcagat	ttatcattctcctgggccttatgtacatct	01/11/07	01/11/07	127	NA	unknown
ss70921198	ILLUMINA\|HumanHap550v3.0__rs729269	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	04/20/07	03/31/08	130	Genomic	unknown
ss71521110	ILLUMINA\|HumanHap650Yv3.0_rs729269	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	04/23/07	04/23/07	127	Genomic	unknown
ss74824415	AFFY\|SNP_M-580127	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	08/09/07	08/09/07	128	Genomic	unknown
ss74925562	ILLUMINA\|ILMN_Human_1M_rs729269	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	08/28/07	08/29/07	129	Genomic	unknown
ss76767955	AFFY\|AFFY_6_1M_SNP_A-8629381	fwd/B	C/T	cccaggagaatgataa	atctgctttgtggtcc	08/28/07	08/30/07	129	Genomic	unknown
ss79253052	ILLUMINA\|HumanHap300v2.0_rs729269	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	04/18/07	11/18/07	130	Genomic	unknown
ss83536858	KRIBB_YJKIM\|KHS484661	fwd/B	C/T	agatgtacataaggcccaggagaatgataa	atctgctttgtggtcctcatgtgtgactat	12/04/07	12/05/07	130	Genomic	unknown

Fasta sequence (Legend)

 TCTGTGGCCT CAACCCAACT GTGGCACTGG GGCCCTGCAG TGGGAGATGC TGTTGAAACA
 CCCAAGCCCA CTGTCCACTG GAACCCCTGC CATGCTGCAG CCGGGGGGCC CTGCCATCCT
 GGAGTGGGGC ATGTGCTCTC TGACATGCTG GAGCGGGGCA TGTGCTCTCT GCCATCCTGG
 AGCAGGGCAT GTACTCTCTG CCATCAAACC TTGGTTCCTT CTTCCAGAAA ACTTTTACAA
 GGTAAATGCT CAGGTCTCCC AAACATACTG AGATGTACAT AAGGCCCAGG AGAATGATAA
 Y
 ATCTGCTTTG TGGTCCTCAT GTGTGACTAT CCAGCCCCCA CTAGTAAGTG ATGGGGACAC
 TCGCAGGCTT TTCCAGGACA GGCAAGGCCA CTGTCTCCAC TTCCTCCATG CTGCCCTGCC
 CTGGCGCCCT GCCTGGAAGC TCTGCCTGCT GGTGCCTCCT CTCCTGGGCA TAGCACAGGT
 GTGTTCCCTC CTCAGTCCAT CGATTCACTC TTCTCCTCAC CCAAATGCTC TGTTTTCGTT
 GGCATCTATC CAGATCCTGC CCTCTTGTAA GCCTCTGCTC AGCTCTCAAC CTTCCAGCAG

GeneView

GeneView via analysis of contig annotation: DPP6 dipeptidyl-peptidase 6

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_034885->NM_001039350

function

CRA_TCAGchr7v2

NT_079596->NM_001936

function

CRA_TCAGchr7v2

NT_079596->NM_130797

function

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


reference	NT_034885->NM_001039350->NP_001034439	141476	forward	intron

CRA_TCAGchr7v2	NT_079596->NM_001936->NP_001927	53776190	forward	intron

CRA_TCAGchr7v2	NT_079596->NM_130797->NP_570629	53776190	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs729269 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839099.2	597938	148244533	plus	T	alt_assembly_8	HuRef	HuRef	view	300
7	NW_923796.1	548549	148929558	minus	G	alt_assembly_1	Celera	Celera	view	300
7	NT_079596.2	53776190	153740622	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	300
7	NT_034885.3	141476	154143043	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034885

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss11878343	CHMJ	Asian	74	IG					0.851	0.149

ss24463435	AFD_EUR_PANEL	European	46	IG	0.652	0.304	0.043	1.000	0.804	0.196

	AFD_AFR_PANEL	African American	46	IG	0.826	0.174		0.655	0.913	0.087

	AFD_CHN_PANEL	Asian	48	IG	0.708	0.292		0.439	0.854	0.146

ss44819001	HapMap-CEU	European	120	IG	0.733	0.233	0.033	0.527	0.850	0.150

	HapMap-HCB	Asian	90	IG	0.622	0.333	0.044	1.000	0.789	0.211

	HapMap-JPT	Asian	88	IG	0.818	0.182		0.527	0.909	0.091

	HapMap-YRI	Sub-Saharan African	120	IG	0.783	0.200	0.017	1.000	0.883	0.117

	AoD_Chinese		90	AF					0.910	0.090

	AoD_Japanese		90	AF					0.850	0.150

ss73990	TSC_42_AA		82	AF					0.890	0.110

	TSC_42_C		84	AF					0.810	0.190

	TSC_42_A		82	AF					0.820	0.180

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.243+/-0.250	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: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .