Reference SNP(refSNP) Cluster Report: rs891921

Reference SNP(refSNP) Cluster Report: rs891921

refSNP ID: rs891921
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_003062.1:c.1112T>C
NP_003053.1:p.V371A
NT_023133.12:g.13022508A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76895097 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs891921 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
ss1321324	TSC-CSHL\|TSC0162982	fwd/B	C/T	tcctgtatgggaacaagatcaccgagattg	caagggactgtttgatgggctggt	09/06/00	10/10/03	86	Genomic	95 %
ss6726044	WI_SSAHASNP\|NT_023132.10_143636	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	02/12/03	10/10/03	111	Genomic	unknown
ss20248380	CSHL-HAPMAP\|CSHL-HuFF-200402.chr5.NT_023133.11_13022509	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	02/21/04	03/04/04	120	Genomic	unknown
ss22251342	SSAHASNP\|WGSA-200403-chr5.chr5.NT_023133.11_13022509	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	03/21/04	03/21/04	121	Genomic	unknown
ss24305560	PERLEGEN\|afd2561480	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	08/10/04	09/13/04	126	Genomic	unknown
ss44677625	ABI\|hCV7512479	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	07/19/05	11/03/06	126	Genomic	unknown
ss48427752	APPLERA_GI\|hCV7512479	fwd/B	C/T	tcctgtatgggaacaagatcaccgagattg	caagggactgtttgatgggctggtgtccct	09/28/05	11/03/06	126	Genomic	unknown
ss65772116	ILLUMINA\|Human1-rs891921	fwd/T	C/T	tcctgtatgggaacaagatcaccgagattg	caagggactgtttgatgggctggt	10/10/06	10/10/06	127	Genomic	unknown
ss68958018	PERLEGEN\|PGP02561480	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	01/30/07	08/14/07	127	Genomic	unknown
ss74809170	AFFY\|SNP_M-181577	fwd/B	C/T	tcctgtatgggaacaagatcaccgagattg	caagggactgtttgatgggctggtgtccct	08/09/07	08/09/07	128	Genomic	unknown
ss74896254	ILLUMINA\|ILMN_Human_1M_rs891921	fwd/B	C/T	tcctgtatgggaacaagatcaccgagattg	caagggactgtttgatgggctggtgtccct	08/28/07	08/29/07	129	Genomic	unknown
ss76502312	AFFY\|AFFY_6_1M_SNP_A-8363418	fwd/B	C/T	aagatcaccgagattg	caagggactgtttgat	08/28/07	08/30/07	129	Genomic	unknown
ss76895097	SI_EXO\|NT_023133.12_13022509	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	09/20/07	09/20/07	129	Genomic	unknown
ss79723110	HGSV\|Cor18507_SNV_20070510.chr5_168145529	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	11/23/07	11/23/07	130	Genomic	unknown
ss82682525	HGSV\|Cor18555_SNV_20070510.chr5_168145529	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	11/27/07	12/03/07	130	Genomic	unknown
ss93329033	BCMHGSC_JDW\|JWB-2072003	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	02/26/08	03/04/08	129	Genomic	unknown
ss109611628	1000GENOMES\|CEU.trio.12.15.2008_1413125_chr5_168145529	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	12/15/08	12/16/08	130	Genomic	unknown
ss113636625	1000GENOMES\|NA19240_2008_12_16_1271356_chr5_168145529	rev/T	A/G	agggacaccagcccatcaaacagtcccttg	caatctcggtgatcttgttcccatacagga	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 ATTGAAGACA CAGGGCCAGT CTCCCACACA GTGTATTTAT TGCTGGGGTG TGAGTCATAT
 TAGCAGCTTA GGGAGATACC ACAAAGAGAC CGCTTCTTCC TGTTGGGGAT TATGTATTGG
 GCTAGGTTGC CCAGGAATGG AGCAGGATAG AGCCCATTTC TACTCACCTC CCAGACAACC
 TGCCCTTCCA GCCCCTGGCT GCTCTTGGCT GCCTCTGTCT CGCTGATGAG AAGGGATTAG
 GCAGGCCGTG GAAGGGGTTG TCCTGAGATC TCATACCCAG AACTGGCCGA GGTGATGGCT
 TCCTGCAGGA CTGGGTTCTG GTGGCCTCAC ATCCACAGTG ATTGCTGTCT TCTCCTTCTC
 TCTTTCAGGG TCCTGTATGG GAACAAGATC ACCGAGATTG
 Y
 CAAGGGACTG TTTGATGGGC TGGTGTCCCT ACAGCTGCTG TGAGTAGGAA CTTTGTCACT
 GTTGGTGTCT TTGGTACTGT CGGAAGGCTC CCACCTGAAA ACGTTGAGCC ATGCTCTGGA
 GAGTTCTTTT GACTTTCTGC AGACAAAAGA GAAAAAAATG TTTGAGCTGT CCACGCTTCA
 CCTCCGTTTC CTATTTTTAT GAAAGGAGAG TCAGCGAGCG GGCAGAGGAA GACCGAGGTC
 AGTGTGCATA AACCCAAATG ATACAGCCGA GGGCCCTGGC CCAGGCATGA AGATACTAAG
 CACAGGGTCT GGGGATAGAG ATTAGGAAAG AGTCAAATCC AACAAAAAGA AAAACATTTT
 TCAGTAGTGT GCTAAGAATG TAAGGAACTA AAACATCCAC

GeneView

GeneView via analysis of contig annotation: SLIT3 slit homolog 3 (Drosophila)

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_023133->NM_003062

function

HuRef

NW_001838954->NM_003062

function

Celera

NW_922784->NM_003062

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_023133->NM_003062->NP_003053	13022509	reverse	1375	missense	C	Ala [A]	2	371
					contig reference	T	Val [V]	2	371

HuRef	NW_001838954->NM_003062->NP_003053	7151732	forward	1375	missense	T	Val [V]	2	371
					contig reference	C	Ala [A]	2	371

Celera	NW_922784->NM_003062->NP_003053	41875753	reverse	1375	missense	T	Val [V]	2	371
					contig reference	C	Ala [A]	2	371

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs891921 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838954.2	7151732	163310593	plus	C	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922784.1	41875753	164247737	minus	G	alt_assembly_1	Celera	Celera	view	300
5	NT_023133.12	13022509	168145529	minus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023133.12 AC027311.3

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_003062.1

UniGene Cluster ID
112631

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24305560	AFD_EUR_PANEL	European	48	IG	0.833	0.167		0.752	0.917	0.083

	AFD_AFR_PANEL	African American	46	IG	0.913	0.087		1.000	0.957	0.043

	AFD_CHN_PANEL	Asian	46	IG	0.913	0.087		1.000	0.957	0.043

ss44677625	HapMap-CEU	European	120	IG	0.817	0.167	0.017	0.584	0.900	0.100

	HapMap-HCB	Asian	90	IG	0.933	0.067		1.000	0.967	0.033

	HapMap-JPT	Asian	88	IG	0.841	0.159		0.584	0.920	0.080

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

ss48427752	AGI_ASP population	multiple	76	IG	0.816	0.184		0.584	0.908	0.092

ss68958018	HapMap-CEU	European	120	GF	0.817	0.167	0.017		0.900	0.100

	HapMap-HCB	Asian	90	GF	0.933	0.067			0.967	0.033

	HapMap-JPT	Asian	90	GF	0.844	0.156			0.922	0.078

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.106+/-0.204	371	299	270	0

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .