Reference SNP(refSNP) Cluster Report: rs9673453

Reference SNP(refSNP) Cluster Report: rs9673453

refSNP ID: rs9673453
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
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_016524.2:c.182+3406C>T
NT_010393.15:g.10501385C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss40658441 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9673453 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
ss13470555	WI_SSAHASNP\|chr16.NT_010393.14_10500639	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	10/31/03	11/10/03	119	Genomic	unknown
ss21333671	SSAHASNP\|WGSA-200403-chr16.chr16.NT_010393.14_10500639	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	03/19/04	03/19/04	121	Genomic	unknown
ss24523657	PERLEGEN\|afd0959876	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	08/10/04	09/13/04	123	Genomic	unknown
ss40658441	ABI\|hCV29947084	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	07/17/05	11/02/06	126	Genomic	unknown
ss66630743	ILLUMINA\|HumanHap300v1.1_rs9673453	fwd/T	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	11/09/06	11/09/06	127	Genomic	unknown
ss67941151	ILLUMINA\|HumanHap550v1.1_rs9673453	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	11/14/06	11/15/06	127	Genomic	unknown
ss68057087	ILLUMINA\|HumanHap650Yv1.0_rs9673453	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	11/14/06	11/15/06	127	Genomic	unknown
ss69340870	PERLEGEN\|PGP00959876	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	01/30/07	03/31/08	127	Genomic	unknown
ss71621838	ILLUMINA\|HumanHap650Yv3.0_rs9673453	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	04/23/07	04/23/07	127	Genomic	unknown
ss75459928	ILLUMINA\|ILMN_Human_1M_rs9673453	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	08/28/07	08/29/07	129	Genomic	unknown
ss79302729	ILLUMINA\|HumanHap300v2.0_rs9673453	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	04/18/07	11/18/07	130	Genomic	unknown
ss84849746	KRIBB_YJKIM\|KHS828794	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	12/04/07	12/08/07	130	Genomic	unknown
ss90341567	BCMHGSC_JDW\|JWB-0928752	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	02/26/08	02/29/08	129	Genomic	unknown
ss98282884	ILLUMINA\|HumanHap550v3.0__rs9673453	fwd/B	C/T	cagagtaaggaatctggattttcttcgata	cagcggagacccctcacaggtgttgagtat	04/20/07	03/31/08	130	Genomic	unknown

Fasta sequence (Legend)

 GACATCACCC CTTGTAGAGA TAGGCGTCTC ATTGTGTTGC CCAGGCTGGT CTTAAACTCC
 TGACCTCAAG CAGTCCTCCC ACCTCAGCCT CCCAAAGCAC TGGGATTACA GGTGAGAGCC
 GCGGCAACCG GCTGTGAATT ATCGCTTGAT TAATGAGTTG CTTTCACCAA AAATCTCAAC
 TCCACACACA CCTGTAGGAT TCAGGCCACA ACTACATCTA GGAAGAGCTG GGGGAGCCTG
 CAAGCTTAGG TTGAGTTGGG TCTTGAATGC CAGAGTAAGG AATCTGGATT TTCTTCGATA
 Y
 CAGCGGAGAC CCCTCACAGG TGTTGAGTAT CACAGCCAGG TACCTGTTTG CCCCCTAGAT
 ATCCAAATGT TGAGTGTTAC AGATGCACAG CCTAGGTTCT CATGCTGAGC TGGAGGACAG
 TTGCGTTTTG CCTTGACTGC TGCTAACCCT TTGTGTAAGC AGGGGCAAGG GGGCTGGGAC
 CCTCTGGGAA GATACTTCTT TTGGTTTTGC CACTAGTAGA GAAGTGGACT GGAACTTTCC
 CAGCAGGGCC AATACACCAC AAAATTCCAG GTGGCGCCAT TCACATGGTG GCCATTATGA

GeneView

GeneView via analysis of contig annotation: SYT17 synaptotagmin XVII

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_010393->NM_016524

function

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


reference	NT_010393->NM_016524->NP_057608	10501385	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9673453 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838381.1	418482	17725706	plus	T	alt_assembly_8	HuRef	HuRef	view	300
16	NW_926151.1	436300	18336165	plus	T	alt_assembly_1	Celera	Celera	view	300
16	NT_010393.15	10501385	19095807	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010393

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
ss24523657	AFD_EUR_PANEL	European	48	IG	0.292	0.625	0.083	0.150	0.604	0.396

	AFD_AFR_PANEL	African American	40	IG	0.150	0.400	0.450	0.655	0.350	0.650

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

ss40658441	HapMap-CEU	European	120	IG	0.467	0.450	0.083	0.752	0.692	0.308

	HapMap-HCB	Asian	90	IG	0.978	0.022		1.000	0.989	0.011

	HapMap-JPT	Asian	88	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	106	IG	0.170	0.396	0.434	0.050	0.368	0.632

ss69340870	HapMap-CEU	European	120	GF	0.467	0.450	0.083		0.692	0.308

	HapMap-HCB	Asian	90	GF	0.978	0.022			0.989	0.011

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.300	0.317	0.383		0.458	0.542

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24523657	71	34	23	11
ss40658441	265	142	68	43
ss69340870	265	153	69	43

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs9673453	332	185	86	53

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5253	ss40658441	C/T	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	r23_ch16_YRI_illumina:infinium_genotyping_2.0.0	5236733
5253	ss69340870	C/C	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	chr16-HapMap-YRI
5254	ss40658441	C/T	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	r23_ch16_YRI_illumina:infinium_genotyping_2.0.0	5236733
5254	ss69340870	C/C	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	chr16-HapMap-YRI
5293	ss40658441	C/T	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r23_ch16_YRI_illumina:infinium_genotyping_2.0.0	5236733
5293	ss69340870	C/C	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	chr16-HapMap-YRI
5309	ss40658441	C/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	r23_ch16_YRI_illumina:infinium_genotyping_2.0.0	5236733
5309	ss69340870	C/C	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	chr16-HapMap-YRI
5310	ss40658441	C/T	CSHL-HAPMAP	HapMap-YRI	NA19129	YOR077.01	r23_ch16_YRI_illumina:infinium_genotyping_2.0.0	5236733
5310	ss69340870	C/C	CSHL-HAPMAP	HapMap-YRI	NA19129	YOR077.01	chr16-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .