Reference SNP(refSNP) Cluster Report: rs9487824

Reference SNP(refSNP) Cluster Report: rs9487824

refSNP ID: rs9487824
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
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_001105206.1:c.3283-570T>C
NM_001105207.1:c.3262-570T>C
NM_002290.3:c.3262-570T>C
NT_025741.14:g.16627455A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss81576437 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9487824 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
ss13128074	SC_SNP\|NT_025741.12_16627455	fwd/T	A/G	tttcattctactttctgaactaatggatga	gttttaagtctacattattgccttttaaga	10/22/03	10/25/06	119	Genomic	unknown
ss23975596	PERLEGEN\|afd0276142	fwd/T	A/G	tttcattctactttctgaactaatggatga	gttttaagtctacattattgccttttaaga	08/10/04	09/13/04	123	Genomic	unknown
ss74853298	AFFY\|SNP_M-613225	fwd/T	A/G	tttcattctactttctgaactaatggatga	gttttaagtctacattattgccttttaaga	08/09/07	08/09/07	128	Genomic	unknown
ss81576437	HGSV\|Cor18956_SNV_20070510.chr6_112564719	fwd/T	A/G	tttcattctactttctgaactaatggatga	gttttaagtctacattattgccttttaaga	11/30/07	11/30/07	130	Genomic	unknown
ss93538958	BCMHGSC_JDW\|JWB-2201885	fwd/T	A/G	tttcattctactttctgaactaatggatga	gttttaagtctacattattgccttttaaga	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 AAATAAGACT GTATTCTTTA TTACTGGAAC TATTTGAAGA CTAAGAAAGT CTCATGAAAT
 TCTTATGAAA TAAAAGTGAC AGTGTCTGGG AGTGGTGGCT CACACCTGTA ATCCCAGCAC
 TCTGGGAGGC CGAGGCAGGT GGATCACTTG AGGCCAGGAG TTTGAGACCA GCCTGGCCAA
 CATGGCAAAA CCTTATCTCT ACTAAAAATA CAAAAACTAG CCAGGCGTGG TGGTAGGCAC
 CTGTAATCCC AGCTACTCAG GGGGCTGAGG CAAGAGAATC GCTTGAACCC GGGAGGTGGA
 AGTTACAGTG AGCCGAGATC GTGACACTGC ACTCCAGCCT GGGCTACAGA ACGAGACTCT
 GTCTCAAAAA AAAAAAAAAA AAGTGACAAC TACTTCCATA TCAGCAGCTA TTTCTCTTAT
 TAATACATAA AAGTTAATAT TTATACACAG TGTAAAAATT CTTCTGTTTT CATTCTACTT
 TCTGAACTAA TGGATGA
 R
 GTTTTAAGTC TACATTATTG CCTTTTAAGA AAATCTTGAA AATAGAGTAT AGTATACCAT
 GTTTATTCAA CTGCCTTGTC TTTAGGAAAC TTTTAAAAAT TATAACAGGC CAACAGATGT
 GTCTGCATTT ATTTTAGGTG AAAATTAGTA AAATTAAAAA ATAATTTCAA GGTATACTGA
 AAAGAATTCT TCCATATTAT

GeneView

GeneView via analysis of contig annotation: LAMA4 laminin, alpha 4

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_025741->NM_001105206

function

reference

NT_025741->NM_001105207

function

reference

NT_025741->NM_002290

function

HuRef

NW_001838990->NM_001105206

function

HuRef

NW_001838990->NM_001105207

function

HuRef

NW_001838990->NM_002290

function

Celera

NW_923184->NM_001105206

function

Celera

NW_923184->NM_001105207

function

Celera

NW_923184->NM_002290

function

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


reference	NT_025741->NM_001105206->NP_001098676	16627455	reverse	intron

reference	NT_025741->NM_001105207->NP_001098677	16627455	reverse	intron

reference	NT_025741->NM_002290->NP_002281	16627455	reverse	intron

HuRef	NW_001838990->NM_001105206->NP_001098676	45089999	forward	intron

HuRef	NW_001838990->NM_001105207->NP_001098677	45089999	forward	intron

HuRef	NW_001838990->NM_002290->NP_002281	45089999	forward	intron

Celera	NW_923184->NM_001105206->NP_001098676	45267941	reverse	intron

Celera	NW_923184->NM_001105207->NP_001098677	45267941	reverse	intron

Celera	NW_923184->NM_002290->NP_002281	45267941	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9487824 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838990.2	45089999	110032899	minus	T	alt_assembly_8	HuRef	HuRef	view	150
6	NT_025741.14	16627455	112564719	plus	A	ref_assembly	reference	reference	view	150
6	NW_923184.1	45267941	113199337	plus	A	alt_assembly_1	Celera	Celera	view	150

NCBI Resource Links

Submitter-Referenced
GenBank
NT_025741

dbSNP Blast Analysis
GenBank HTGS Finished:
NC_000006.10 Z99289.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss13128074	HapMap-CEU	European	120	IG	0.800	0.133	0.067	0.003	0.867	0.133

	HapMap-HCB	Asian	90	IG	0.444	0.444	0.111	1.000	0.667	0.333

	HapMap-JPT	Asian	90	IG	0.267	0.511	0.222		0.522	0.478

	HapMap-YRI	Sub-Saharan African	120	IG	0.917	0.083		0.752	0.958	0.042

ss23975596	AFD_EUR_PANEL	European	48	IG	0.667	0.333		0.343	0.833	0.167

	AFD_AFR_PANEL	African American	46	IG	0.696	0.304		0.403	0.848	0.152

	AFD_CHN_PANEL	Asian	48	IG	0.458	0.375	0.167	0.403	0.646	0.354

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.348+/-0.230	332	260	9	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 .