Reference SNP(refSNP) Cluster Report: rs1448424

Reference SNP(refSNP) Cluster Report: rs1448424

refSNP ID: rs1448424
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002210.2:c.1159+1657C>T
NT_005403.16:g.37717389C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2263324 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1448424 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
ss2263324	TSC-CSHL\|TSC0673947	fwd/T	A/G	ctgttgtctatatttgttctactgacagac	acacattataacaaaaacttagaaagctgg	10/20/00	04/07/04	88	Genomic	95 %
ss6182380	SC_JCM\|NT_005265.10_7289792	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	01/10/03	10/10/03	111	Genomic	unknown
ss14511812	WUGSC_SSAHASNP\|chr2.NT_005403.14_37717388	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	11/05/03	11/22/03	119	Genomic	unknown
ss16874155	CSHL-HAPMAP\|CSHL-HuAA-200402.chr2.NT_005403.14_37717388	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	02/17/04	03/04/04	120	Genomic	unknown
ss19461788	CSHL-HAPMAP\|CSHL-HuDD-200402.chr2.NT_005403.14_37717388	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	02/20/04	03/04/04	120	Genomic	unknown
ss20113777	CSHL-HAPMAP\|CSHL-HuFF-200402.chr2.NT_005403.14_37717388	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	02/21/04	03/04/04	120	Genomic	unknown
ss21711829	SSAHASNP\|WGSA-200403-chr2.chr2.NT_005403.14_37717388	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	03/20/04	03/20/04	121	Genomic	unknown
ss24639670	PERLEGEN\|afd1392010	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	08/10/04	09/13/04	123	Genomic	unknown
ss44147773	ABI\|hCV1278125	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	07/18/05	11/03/06	126	Genomic	unknown
ss91478172	BCMHGSC_JDW\|JWB-1357163	rev/B	C/T	ccagctttctaagtttttgttataatgtgt	gtctgtcagtagaacaaatatagacaacag	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 TTCATGCAAT TGATTTCTTC CTTTGATCAT TTTAGATGCT CTTTCCTGCT TTTCTTTTTT
 TTCCTCTGCT TTTTCTGGAA AAGTACTGAT AAAAAACTGC ACATAATTAC CTTGGGGCTA
 TATAAAATTT TGGAACATAA CTTTATTGTT TTGTTTTCAA TATCCCTCTT GATGATGCCT
 AGGGTGGGGG TAGGTGGAAA GAGAGGAATA TAGGAATACA GGAACAATGA CACTTAATGT
 CTTCATGTAT GAACAACAAC AAAAGATCTA ACATAACTAA TAGAACATAT ACATGTATAA
 TGTAACTATA TTTGCACATA TGTACTAAAT ACTATACATA AATACAGCTC AGATAATTTT
 TCACTAAAGA CATTATCATT CACAATCTAC TATTTGCTAC AGTAAGACCC AAGGAGAAAC
 CTTGGGAGAC CATAATCATC CTCTATGGAT GATTTTATCT ATATTTTAGC CCTTTGTAAA
 ATCATTGTAA AACTTCACAT TTTTTAAAGC TGTTGTCTAT ATTTGTTCTA CTGACAGAC
 R
 ACACATTATA ACAAAAACTT AGAAAGCTGG AAGAGATGTT GGCTAGATCA CAGTAATGAG
 AAAACTTT

GeneView

GeneView via analysis of contig annotation: ITGAV integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)

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_005403->NM_002210

function

HuRef

NW_001838863->NM_002210

function

Celera

NW_921585->NM_002210

function

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


reference	NT_005403->NM_002210->NP_002201	37717389	forward	intron

HuRef	NW_001838863->NM_002210->NP_002201	12924139	forward	intron

Celera	NW_921585->NM_002210->NP_002201	55293444	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1448424 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838863.1	12924139	179367833	minus	C	alt_assembly_8	HuRef	HuRef	view	539
2	NW_921585.1	55293444	181103641	minus	T	alt_assembly_1	Celera	Celera	view	539
2	NT_005403.16	37717389	187216217	minus	C	ref_assembly	reference	reference	view	539

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005403

dbSNP Blast Analysis
GenBank HTGS Finished:
AC017101.10 NC_000002.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss2263324	SC_12_A	Asian	20	IG	1.000				1.000

	SC_12_C	European	14	IG	0.714	0.286		0.752	0.857	0.143

	HapMap-CEU	European	120	IG	0.483	0.383	0.133	0.343	0.675	0.325

	HapMap-HCB	Asian	90	IG	0.667	0.333		0.200	0.833	0.167

	HapMap-JPT	Asian	88	IG	0.795	0.205		0.479	0.898	0.102

	HapMap-YRI	Sub-Saharan African	120	IG	0.783	0.183	0.033	0.251	0.875	0.125

ss24639670	AFD_EUR_PANEL	European	46	IG	0.304	0.652	0.043	0.100	0.630	0.370

	AFD_AFR_PANEL	African American	44	IG	0.682	0.318		0.403	0.841	0.159

	AFD_CHN_PANEL	Asian	48	IG	0.708	0.292		0.439	0.854	0.146

ss44147773	AoD_Chinese		90	AF					0.800	0.200

	AoD_Japanese		90	AF					0.910	0.090

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss2263324	291	188	88	12
ss24639670	71

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1448424	354	188	88	12

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
229	ss2263324	A/A	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	286700
229	ss2263324	A/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch2_CEU_illumina:golden_gate_1.0.0	286700

Genotype data submitted for	365	samples from	354	individuals	Individual with multiple genotypes submission:	11

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA, PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .