Reference SNP(refSNP) Cluster Report: rs7454457

Reference SNP(refSNP) Cluster Report: rs7454457

refSNP ID: rs7454457
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
Map to Genome Build:	36.3

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

HGVS Names
NM_018303.4:c.-44+24392T>G
NT_034880.3:g.608627A>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss11258357 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7454457 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
ss11258357	SC_JCM\|chr6.NT_034880.2_608627	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	07/03/03	04/07/04	116	Genomic	unknown
ss12892094	SC_SNP\|NT_034880.2_608627	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	10/21/03	10/31/03	119	Genomic	unknown
ss15734171	SC_SNP\|NT_034880.3_608627	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	11/17/03	11/22/03	120	Genomic	unknown
ss17134041	CSHL-HAPMAP\|CSHL-HuAA-200402.chr6.NT_034880.3_608627	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	02/17/04	03/04/04	120	Genomic	unknown
ss22427043	SSAHASNP\|WGSA-200403-chr6.chr6.NT_034880.3_608627	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	03/21/04	03/21/04	121	Genomic	unknown
ss24415117	PERLEGEN\|afd4615977	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	08/10/04	09/13/04	123	Genomic	unknown
ss44731871	ABI\|hCV30250609	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	07/19/05	07/19/05	126	Genomic	unknown
ss66297838	AFFY\|SNP_A-1839038	rev/B	G/T	tagagataagtataca	ggggtacgattaatcc	10/29/06	03/31/08	127	Genomic	unknown
ss66723725	ILLUMINA\|HumanHap300v1.1_rs7454457	fwd/B	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	11/09/06	11/09/06	127	Genomic	unknown
ss67579891	ILLUMINA\|HumanHap550v1.1_rs7454457	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	11/14/06	11/14/06	127	Genomic	unknown
ss67961730	ILLUMINA\|HumanHap650Yv1.0_rs7454457	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	11/14/06	11/15/06	127	Genomic	unknown
ss70928510	ILLUMINA\|HumanHap550v3.0__rs7454457	rev/B	G/T	tactggctgaatggtagagataagtataca	ggggtacgattaatccaacctggggctgag	04/20/07	03/31/08	130	Genomic	unknown
ss71529740	ILLUMINA\|HumanHap650Yv3.0_rs7454457	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	04/23/07	04/23/07	127	Genomic	unknown
ss75662414	ILLUMINA\|ILMN_Human_1M_rs7454457	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	08/28/07	08/29/07	129	Genomic	unknown
ss75967417	AFFY\|AFFY_6_1M_SNP_A-1839038	rev/B	G/T	tagagataagtataca	ggggtacgattaatcc	08/28/07	08/29/07	129	Genomic	unknown
ss79257469	ILLUMINA\|HumanHap300v2.0_rs7454457	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	04/18/07	11/18/07	130	Genomic	unknown
ss84666210	KRIBB_YJKIM\|KHS773681	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	12/04/07	12/07/07	130	Genomic	unknown
ss85211860	HGSV\|Cor19129_SNV_20070510.chr6_613627	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	12/06/07	12/08/07	130	Genomic	unknown
ss93363920	BCMHGSC_JDW\|JWB-2085732	fwd/T	A/C	ctcagccccaggttggattaatcgtacccc	tgtatacttatctctaccattcagccagta	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 GCCCTGTGCT CACTGCTGAA ATCTGCGTTC TGTCACACTC AGCGTTAGGT CCCTCAACAC
 CCATCCCACC TGCTTCTTAG CCAACTAACT TCCACCATTC ACCCATTCAG TCATCACTTT
 CTGTGGGAAG CTACACCTTC CCTCACCTCA CTTCCAACAA CCTAACCTCC CTCAGCCCCA
 GGTTGGATTA ATCGTACCCC
 M
 TGTATACTTA TCTCTACCAT TCAGCCAGTA AAAGTAGAGA TACTATGgtc tcttgggatc
 taccagtaat tcgtcctaag gcattctgtg gataccaaaa tctggggatg ctcaggttcc
 ctacataaaa ttgcatagta tttgcatata acccacacac atccaccagc atactctaga
 ttactaatca tctctagatt acttataata cataatacaa tgtaagttat caaactgtat
 tgtttttgtt gtttttttat tgctgcattg tttttttctg aatattttcc atctgtgatt
 ggttgaatct gtccatgcag aacccatgga tatggagagc tgactgTATT TCTTTTTTAC
 TTACTTGGTG CTAGGCACAT GAAGGTGCGG AATAAACGCT TATGAATGAA CCTCCAACTG
 GTATGTTTGC TCCTCGAGGA CAAGTATTAC CACCTGCAAC TGTCTGCATC CCACACCCGG
 CTGATCTCCT GCACCATGT

GeneView

GeneView via analysis of contig annotation: EXOC2 exocyst complex component 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_034880->NM_018303

function

HuRef

NW_001838972->NM_018303

function

Celera

NW_922984->NM_018303

function

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


reference	NT_034880->NM_018303->NP_060773	608627	reverse	intron

HuRef	NW_001838972->NM_018303->NP_060773	3117600	forward	intron

Celera	NW_922984->NM_018303->NP_060773	291246	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs7454457 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838972.2	3117600	537264	minus	G	alt_assembly_8	HuRef	HuRef	view	200
6	NT_034880.3	608627	613627	plus	A	ref_assembly	reference	reference	view	200
6	NW_922984.1	291246	1895990	plus	C	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034880

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL357054.14 NC_000006.10	AL138738.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C	N
ss11258357	HapMap-CEU	European	112	IG	0.179	0.482	0.339	1.000	0.420	0.580

	HapMap-HCB	Asian	90	IG	0.022	0.311	0.667	0.752	0.178	0.822

	HapMap-JPT	Asian	88	IG		0.386	0.614	0.150	0.193	0.807

	HapMap-YRI	Sub-Saharan African	120	IG	0.283	0.500	0.217	1.000	0.533	0.467

	CHMJ	Asian	74	IG					0.203	0.770	0.027

ss24415117	AFD_EUR_PANEL	European	48	IG	0.250	0.292	0.458	0.100	0.396	0.604

	AFD_AFR_PANEL	African American	46	IG	0.174	0.391	0.435	0.479	0.370	0.630

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.208	0.750	0.439	0.146	0.854

ss66297838	HapMap-CEU	European	118	GF	0.186	0.475	0.339		0.424	0.576

	HapMap-HCB	Asian	90	GF	0.022	0.311	0.667		0.178	0.822

	HapMap-JPT	Asian	90	GF		0.422	0.578		0.211	0.789

	HapMap-YRI	Sub-Saharan African	120	GF	0.283	0.500	0.217		0.533	0.467

Concordant Genotype	Total Sample	A/A	A/C	C/C
ss11258357	267	45	117	100
ss24415117	70	11	21	38
ss66297838	266

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C
rs7454457	332	52	135	137

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
175	ss11258357	C/C	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	r23_ch6_CEU_illumina:golden_gate_1.0.0	499895
175	ss66297838	G/T	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	chr6-HapMap-CEU
242	ss11258357	C/C	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	r23_ch6_CEU_illumina:golden_gate_1.0.0	499895
242	ss24415117	C/C	PERLEGEN	AFD_EUR_PANEL	NA10854		71_IND_CHR_6
242	ss66297838	G/T	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	chr6-HapMap-CEU
5233	ss11258357	C/C	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	r23_ch6_JPT_illumina:golden_gate_1.0.0	499895
5233	ss66297838	G/T	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	chr6-HapMap-JPT

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	269

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .