Reference SNP(refSNP) Cluster Report: rs7538840

Reference SNP(refSNP) Cluster Report: rs7538840

refSNP ID: rs7538840
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_001079874.1:c.97+15311A>G
NM_006113.4:c.1777+15311A>G
NT_019273.18:g.4118484T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44036594 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7538840 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
ss11395996	WI_SSAHASNP\|chr1.NT_029860.10_3207941	fwd/B	C/T	tagcctacttcatctcacttcctccctcca	tgagcatctggcatgatccataattgtagc	07/03/03	10/10/03	116	Genomic	unknown
ss15556967	SC_SNP\|NT_029860.11_4286910	fwd/B	C/T	tagcctacttcatctcacttcctccctcca	tgagcatctggcatgatccataattgtagc	11/17/03	11/22/03	120	Genomic	unknown
ss17344096	CSHL-HAPMAP\|CSHL-HuCC-200402.chr1.NT_029860.11_4286910	fwd/B	C/T	tagcctacttcatctcacttcctccctcca	tgagcatctggcatgatccataattgtagc	02/19/04	03/04/04	120	Genomic	unknown
ss20513589	SSAHASNP\|WGSA-200403-chr1.chr1.NT_029860.11_4286910	fwd/B	C/T	tagcctacttcatctcacttcctccctcca	tgagcatctggcatgatccataattgtagc	03/18/04	03/18/04	121	Genomic	unknown
ss23853772	PERLEGEN\|afd1082956	fwd/B	C/T	tagcctacttcatctcacttcctccctcca	tgagcatctggcatgatccataattgtagc	08/10/04	09/13/04	123	Genomic	unknown
ss44036594	ABI\|hCV93117	fwd/B	C/T	tagcctacttcatctcacttcctccctcca	tgagcatctggcatgatccataattgtagc	07/18/05	11/03/06	126	Genomic	unknown

Fasta sequence (Legend)

 TGCTTGGAAT CGTAGCATCC CAAGGTTGGC AGAGACTTGA GGGGCCATCT GCAGTGTCTG
 CTTGCCCTTT GCCCAACTGG GCCCTTCCGA GAAGCTCTTT CCCAGGCTCT CCAATCACCT
 CAGCTGGTCC TCTCTCATCC AGGACCCAGA CAGTCATATG ATAGCAACCC TGCCTTAAGC
 CTTCACATCA AGGTCATATT TCTCCTTTCA TTTGATATTG ACAATTAAGA GTGCTTATCC
 TTCTTCAATC TGACCAAGAT TATTTCTCTT TAGCCTACTT CATCTCACTT CCTCCCTCCA
 Y
 TGAGCATCTG GCATGATCCA TAATTGTAGC CAGCCTGGCT AAAAAATAAA TCTTCTGATA
 AAGTGCACTG ATTTAATGAA TGCATTCCTA CAAGACTGCT AAATTAGTTA AAAACATACA
 ATGCTTCTTC TAGTTATGGA AACACATATA TGGAAGTTTT ATAAGGATTT GGTTTAAAGC
 TCAGTTTCAG CGTTTATTAC TTACATGAAT TTGGACACCT GTCACAACTC TCAGTGTAGC
 TTCCTCATCT GTAAAATGGG CATAATACCT CTCACAGCTT TGTTGTGAAA TTAAAAATAA

GeneView

GeneView via analysis of contig annotation: VAV3 vav 3 guanine nucleotide exchange factor

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_019273->NM_001079874

function

reference

NT_019273->NM_006113

function

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


reference	NT_019273->NM_001079874->NP_001073343	4118484	reverse	intron

reference	NT_019273->NM_006113->NP_006104	4118484	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs7538840 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838590.2	565154	106156697	minus	G	alt_assembly_8	HuRef	HuRef	view	300
1	NW_922017.1	3915854	106385526	plus	T	alt_assembly_1	Celera	Celera	view	300
1	NT_019273.18	4118484	108012322	plus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029860

dbSNP Blast Analysis
GenBank HTGS Finished:
AL513206.6

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23853772	AFD_EUR_PANEL	European	48	IG	0.542	0.292	0.167	0.150	0.688	0.312

	AFD_AFR_PANEL	African American	46	IG	0.478	0.478	0.043	0.403	0.717	0.283

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.500	0.375	0.752	0.375	0.625

ss44036594	AoD_African_American		90	AF					0.670	0.330

	AoD_Caucasian		92	AF					0.610	0.390

	AoD_Chinese		90	AF					0.440	0.560

	AoD_Japanese		90	AF					0.310	0.690

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.483+/-0.090	71	50	0	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 .