Reference SNP(refSNP) Cluster Report: rs178173

Reference SNP(refSNP) Cluster Report: rs178173

refSNP ID: rs178173
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:	A/C
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_002515.2:c.281-53723C>A
NM_006489.2:c.281-53723C>A
NM_006491.2:c.281-53723C>A
NT_026437.11:g.8002912G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss89886500 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs178173 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
ss237040	KWOK\|OVLP-000621-245733	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	06/30/00	10/10/03	79	Genomic	94 %
ss493083	SC_JCM\|AL132716.4_48288	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	07/12/00	10/10/03	80	Genomic	unknown
ss1274604	KWOK\|OVLP-000804-448666	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	09/02/00	10/10/03	86	Genomic	94 %
ss1882708	KWOK\|OVLP-000925-217962	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	10/06/00	10/25/06	87	Genomic	99 %
ss3890140	SC_JCM\|AL133316.3_35214	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	09/25/01	10/10/03	100	Genomic	unknown
ss10724386	BCM_SSAHASNP\|chr14.NT_026437.10_6923200	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	06/30/03	10/10/03	116	Genomic	unknown
ss12272497	WI_SSAHASNP\|chr14.NT_026437.10_6923200	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	07/04/03	10/10/03	116	Genomic	unknown
ss16648619	CSHL-HAPMAP\|CSHL-HuAA-200402.chr14.NT_026437.10_6923200	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	02/17/04	03/04/04	120	Genomic	unknown
ss19300078	CSHL-HAPMAP\|CSHL-HuDD-200402.chr14.NT_026437.10_6923200	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	02/20/04	03/04/04	120	Genomic	unknown
ss19988542	CSHL-HAPMAP\|CSHL-HuFF-200402.chr14.NT_026437.10_6923200	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	02/21/04	03/04/04	120	Genomic	unknown
ss21156223	SSAHASNP\|WGSA-200403-chr14.chr14.NT_026437.10_6923200	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	03/19/04	03/19/04	121	Genomic	unknown
ss23621302	PERLEGEN\|afd4653796	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	08/10/04	09/13/04	123	Genomic	unknown
ss66381303	AFFY\|SNP_A-2042783	rev/B	G/T	aactctctgagaacaa	gtaaattatcaaaatt	10/29/06	08/14/07	127	Genomic	unknown
ss67195289	ILLUMINA\|HumanHap550v1.1_rs178173	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	11/14/06	11/14/06	127	Genomic	unknown
ss67581952	ILLUMINA\|HumanHap650Yv1.0_rs178173	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	11/14/06	11/14/06	127	Genomic	unknown
ss68187961	ILLUMINA\|HumanHap250Sv1.0_rs178173	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	12/06/06	12/07/06	127	Genomic	unknown
ss70673484	ILLUMINA\|HumanHap550v3.0__rs178173	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	04/20/07	03/30/08	130	Genomic	unknown
ss71236208	ILLUMINA\|HumanHap650Yv3.0_rs178173	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	04/23/07	04/23/07	127	Genomic	unknown
ss75492800	ILLUMINA\|ILMN_Human_1M_rs178173	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	08/28/07	08/29/07	129	Genomic	unknown
ss76115242	AFFY\|AFFY_6_1M_SNP_A-2042783	rev/B	G/T	aactctctgagaacaa	gtaaattatcaaaatt	08/28/07	08/30/07	130	Genomic	unknown
ss77117713	HGSV\|Cor12156_SNV_20070510.chr14_26072912	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	10/09/07	10/11/07	129	Genomic	unknown
ss78024915	HGSV\|Cor12878_SNV_20070510.chr14_26072912	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	10/17/07	10/17/07	129	Genomic	unknown
ss83377850	KRIBB_YJKIM\|KHS447207	fwd/T	A/C	gctatttttgagtgaattttgataatttac	ttgttctcagagagttgtccactctatcaa	12/04/07	12/04/07	130	Genomic	unknown
ss89886500	BCMHGSC_JDW\|JWB-0750762	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	02/26/08	02/28/08	129	Genomic	unknown
ss108192907	1000GENOMES\|CEU.trio.12.15.2008_3011409_chr14_26072912	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	12/15/08	12/15/08	130	Genomic	unknown
ss115432106	1000GENOMES\|NA19240_2008_12_16_2698995_chr14_26072912	rev/B	G/T	ttgatagagtggacaactctctgagaacaa	gtaaattatcaaaattcactcaaaaatagc	12/18/08	12/19/08	130	Genomic	unknown

Fasta sequence (Legend)

 CTTTCTTTTC CATTTTGATT ATCAGAGTTA TGCTAGTTAT TAGTAAAGTG AATTTAAAGA
 CATTCTATTT TTCCTCTATA GACTAGTTTA TATTCAGTAT TGAATACTTT TTGTAGCATG
 AAAATTCTCT TTGCATTTAT AGTTTGAAAT ATCACATACA GCAGTCTGAG CACAGAGCTT
 ATTTGAATAT ATTTATTTGA TAGGCCTTTT TCATTTCTTG GCTATTTTTG AGTGAATTTT
 GATAATTTAC
 M
 TTGTTCTCAG AGAGTTGTCC ACTCTATCAA GATTTTACAG GACTATTTGT TGCATACCTG
 CTATGTATTA AGCATTGTGC TAGGTGCTGT GCATGCAAAG ATAAGAATTT CCTAGGATTC
 TTAATCTCAG GAAGCATGTA GTGAGAGAAG TTAATTTTCT TAGGGTAGAG ACATAAGAAA
 TAGAAAAGAA GAAATTAACA TCTAAACAGA ACTTCTGATA ACGATTTCCT CATGAATACA
 GGCAGCATGT

GeneView

GeneView via analysis of contig annotation: NOVA1 neuro-oncological ventral antigen 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_026437->NM_002515

function

reference

NT_026437->NM_006489

function

reference

NT_026437->NM_006491

function

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


reference	NT_026437->NM_002515->NP_002506	8002912	reverse	intron

reference	NT_026437->NM_006489->NP_006480	8002912	reverse	intron

reference	NT_026437->NM_006491->NP_006482	8002912	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs178173 maps exactly once on NCBI human chromosome 14

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
14	NW_925539.1	6809600	6867478	minus	T	alt_assembly_1	Celera	Celera	view	250
14	NW_001838110.1	6807904	7119080	minus	T	alt_assembly_8	HuRef	HuRef	view	250
14	NT_026437.11	8002912	26072912	minus	G	ref_assembly	reference	reference	view	250

NCBI Resource Links

Submitter-Referenced
GenBank
NT_026437 AL132716 AL133316 AL133316.2 AL133316.3

dbSNP Blast Analysis
GenBank HTGS Finished:
AL132716.6 AL133316.5

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss1882708	HapMap-CEU	European	120	IG	1.000				1.000

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.483	0.500	0.017	0.050	0.733	0.267

ss23621302	AFD_EUR_PANEL	European	48	IG	1.000				1.000

	AFD_AFR_PANEL	African American	46	IG	0.739	0.261		0.479	0.870	0.130

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

ss493083	SC_12_A	Asian	20	IG	1.000				1.000

	SC_12_AA	African American	20	IG	0.900	0.100		1.000	0.950	0.050

	SC_12_C	European	8	IG	1.000				1.000

ss66381303	HapMap-CEU	European	118	GF	1.000				1.000

	HapMap-HCB	Asian	90	GF	1.000				1.000

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.483	0.500	0.017		0.733	0.267

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.129+/-0.219	360	279	275	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .