Reference SNP(refSNP) Cluster Report: rs6830813

Reference SNP(refSNP) Cluster Report: rs6830813

refSNP ID: rs6830813
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/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_032432.3:c.900+458C>T
NT_006051.17:g.4133877G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10138024 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6830813 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
ss10138024	BCM_SSAHASNP\|chr4.NT_006307.14_159901	fwd/T	A/G	tctctctctctctctcgaacgaacgaaaac	ggatcacataatttacatcacccttaactt	06/27/03	10/25/06	116	Genomic	unknown
ss68890105	PERLEGEN\|PGP03406833	fwd/T	A/G	tctctctctctctctcgaacgaacgaaaac	ggatcacataatttacatcacccttaactt	01/30/07	03/31/08	127	Genomic	unknown
ss77149587	HGSV\|Cor12156_SNV_20070510.chr4_8164504	fwd/T	A/G	tctctctctctctctcgaacgaacgaaaac	ggatcacataatttacatcacccttaactt	10/09/07	10/11/07	129	Genomic	unknown
ss78538943	HGSV\|Cor18507_SNV_20070510.chr4_8164504	fwd/T	A/G	tctctctctctctctcgaacgaacgaaaac	ggatcacataatttacatcacccttaactt	10/19/07	10/19/07	129	Genomic	unknown
ss84290966	HGSV\|Cor18517_SNV_20070510.chr4_8164504	fwd/T	A/G	tctctctctctctctcgaacgaacgaaaac	ggatcacataatttacatcacccttaactt	12/06/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 TTACACAAGC AATATTAGCA AACATTAAAT ACAATATTAA ATATtaaatt tacatataca
 tatgtatatg tatgtataca tatataaatt taaatataca ATATTAAATG TATTAAATAT
 TAAATAGAAT AATCTCCCAT CTCGAATCCC ACCACCCAGA GGAAATTTCT GGTAACAACT
 TGTTAAAATG TTTTCAATCA TTTTTATATT TGTATGTGAT TATGGAAGCG TGTGAGGCGc
 acagacacac acacacacac acacacacaG AGtctctctc tctctctctc tctcGAACGA
 ACGAAAAC
 R
 GGATCACATA ATTTACATCA CCCTTAACTT GCTTCTTTTA GGGAACACGC TGGGAGAGCG
 TGCGTGTTGA TGTACACAGA TCCGTGCCGT TATTTGCAAA CTCTGCAGGG TCCCGCCTGG
 GTGTCTGGCA AGCCCCAACT GTCGGCTGTT GATGTGACGT GTCTGCACCA CTATAAACAA
 CAGCTGTGTA CACACCACTG

GeneView

GeneView via analysis of contig annotation: ABLIM2 actin binding LIM protein family, member 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_006051->NM_032432

function

HuRef

NW_001838899->NM_032432

function

Celera

NW_921918->NM_032432

function

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


reference	NT_006051->NM_032432->NP_115808	4133877	reverse	intron

HuRef	NW_001838899->NM_032432->NP_115808	178824	reverse	intron

Celera	NW_921918->NM_032432->NP_115808	7946147	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6830813 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_921918.1	7946147	7946147	plus	G	alt_assembly_1	Celera	Celera	view	308
4	NW_001838899.1	178824	7966176	plus	G	alt_assembly_8	HuRef	HuRef	view	308
4	NT_006051.17	4133877	8097333	plus	G	ref_assembly	reference	reference	view	308

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006307

dbSNP Blast Analysis
GenBank HTGS Finished:
AC097381.3 NC_000004.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss10138024	HapMap-CEU	European	108	IG	0.148	0.315	0.537	0.100	0.306	0.694

	HapMap-HCB	Asian	88	IG		0.023	0.977	1.000	0.011	0.989

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.267	0.433	0.300	0.317	0.483	0.517

ss68890105	HapMap-CEU	European	120	GF	0.150	0.350	0.500		0.325	0.675

	HapMap-HCB	Asian	90	GF		0.022	0.978		0.011	0.989

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.267	0.433	0.300		0.483	0.517

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss10138024	269	35	64	155
ss68890105	269	36	74	159

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs6830813	270	36	74	159

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
611	ss10138024	A/G	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	r23_ch4_CEU_perlegen:genotyping_1.0.0	2750906
611	ss68890105	G/G	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	chr4-HapMap-CEU

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	270

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 .