Reference SNP(refSNP) Cluster Report: rs1057139

Reference SNP(refSNP) Cluster Report: rs1057139

refSNP ID: rs1057139
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/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_001003407.1:c.*243G>C
NM_001003408.1:c.*243G>C
NM_002313.5:c.*243G>C
NM_006720.3:c.*243G>C
NT_030059.12:g.34944302C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52067714 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1057139 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
ss1537578	LEE\|707574	fwd/T	C/G	tccgaaacacagagtagtgtccacatgtga	cttttcacattaccttatgtatacaacagg	09/13/00	10/10/03	86	cDNA	unknown
ss4320737	CGAP-GAI\|235890	fwd/T	C/G	tccgaaacacagagtagtgtccacatgtga	cttttcacattaccttatgtatacaacagg	11/28/01	10/10/03	102	cDNA	unknown
ss4425450	LEE\|e707574	fwd/T	C/G	tccgaaacacagagtagtgtccacatgtga	cttttcacattaccttatgtatacaacagg	04/26/02	10/10/03	106	cDNA	unknown
ss4989122	YUSUKE\|IMS-JST161481	rev/B	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	08/12/02	11/22/03	108	Genomic	unknown
ss12077191	WI_SSAHASNP\|chr10.NT_030059.10_34634334	rev/B	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	07/04/03	05/16/04	116	Genomic	unknown
ss15991168	SC_SNP\|NT_030059.11_34944302	rev/B	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	11/18/03	11/22/03	120	Genomic	unknown
ss17382722	CSHL-HAPMAP\|CSHL-HuCC-200402.chr10.NT_030059.11_34944302	rev/B	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	02/19/04	03/04/04	120	Genomic	unknown
ss24125023	PERLEGEN\|afd2306249	rev/B	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	08/10/04	09/13/04	123	Genomic	unknown
ss38556579	ABI\|hCV1304830	rev/	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	07/15/05	11/02/06	126	Genomic	unknown
ss52067714	SI_EXO\|NT_030059.12_34944302	rev/	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	03/29/06	08/14/07	127	Genomic	unknown
ss80639373	HGSV\|Cor18507_SNV_20070510.chr10_116185766	rev/	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	11/23/07	11/26/07	130	Genomic	unknown
ss88363125	BCMHGSC_JDW\|JWB-0337860	rev/	C/G	cctgttgtatacataaggtaatgtgaaaag	tcacatgtggacactactctgtgtttcgga	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 CATCAGGACT GACAGCAGCT CTTTTTTTTT TTTCTTCTTC CCAGCGCCAC TTAGCCCCTG
 AAGTGTTTCG GGAAATCTTT GGAATGTCCA TACAGGAGTT TGACAGGTTA CCTCTTTGGA
 GACGCAACGA CATGAAGAAA AAAGCAAAAC TCTTCTAAGT CCCACTCGTG AATGGCAATT
 AGAGAAAGGA CTGACAGTGG CGGTGCCCCA TAGGATGTCA TATTGAGGCC CAAACTTGAT
 TGGAGAATTT GCAAACTACC GTCGCTCAGC AACACCAAAA AGAGAAAGTC TGGTTAAAAC
 ACCATGAGTC AAATGTCGGG CCAGCCAACA GTAACACTTG CCAAGAAGCA TGGCGTAGAA
 ATTTCTATGT TCCGAAACAC AGAGTAGTGT CCACATGTGA
 S
 CTTTTCACAT TACCTTATGT ATACAACAGG AGCTGCGTTG TTTTCTTCTT TTTCTTTTCC
 TTTATCTGTT GTCCAACAAC AGTGCTGACT GTCCGGATAA GAGCTGGCAA GTGCCCTTAG
 GATGCCGCAT GGGAAAAATC GGTTATCATA ATTTCAAAGT ATAAATATAT TTATTAAGTA
 GCGCTGCGGC TAAGAAGGAA GAGTGAGGGG TCTGTCCATG GGGTGGCAGT GATTTCACAC
 CCGCCTTTCT TGAATGGCTT CGTGTTACTC AGCCGTGCCC TGGCAGGAAT GGAACTCCAT
 CAGGGAACAG GGCAGCTCTG TTTGAATGGG GTGAAAAACA GCAAAATTAA TTCTTAGCAA
 GCTCCTTGTT CTCTACTGTT CACCGGGACC TGGCTGGCAA

GeneView

GeneView via analysis of contig annotation: ABLIM1 actin binding LIM protein 1

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_030059->NM_001003407

function

reference

NT_030059->NM_001003408

function

reference

NT_030059->NM_002313

function

reference

NT_030059->NM_006720

function

HuRef

NW_001838006->NM_001003407

function

HuRef

NW_001838006->NM_001003408

function

HuRef

NW_001838006->NM_002313

function

HuRef

NW_001838006->NM_006720

function

Celera

NW_924884->NM_001003407

function

Celera

NW_924884->NM_001003408

function

Celera

NW_924884->NM_002313

function

Celera

NW_924884->NM_006720

function

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


reference	NT_030059->NM_001003407->	34944302	reverse	2702	3' UTR

reference	NT_030059->NM_001003408->	34944302	reverse	2786	3' UTR

reference	NT_030059->NM_002313->	34944302	reverse	2679	3' UTR

reference	NT_030059->NM_006720->	34944302	reverse	1932	3' UTR

HuRef	NW_001838006->NM_001003407->	8809165	forward	2702	3' UTR

HuRef	NW_001838006->NM_001003408->	8809165	forward	2786	3' UTR

HuRef	NW_001838006->NM_002313->	8809165	forward	2679	3' UTR

HuRef	NW_001838006->NM_006720->	8809165	forward	1932	3' UTR

Celera	NW_924884->NM_001003407->	26927831	reverse	2702	3' UTR

Celera	NW_924884->NM_001003408->	26927831	reverse	2786	3' UTR

Celera	NW_924884->NM_002313->	26927831	reverse	2679	3' UTR

Celera	NW_924884->NM_006720->	26927831	reverse	1932	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1057139 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_001838006.2	8809165	109822519	plus	G	alt_assembly_8	HuRef	HuRef	view	400
10	NW_924884.1	26927831	109925014	minus	C	alt_assembly_1	Celera	Celera	view	400
10	NT_030059.12	34944302	116185766	minus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
CGAP-C-23589	NT_030059.12 Hs.158203

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_001003407.1 NM_001003408.1 NM_002313.5 NM_006720.3	AL133384.12 NC_000010.9	BC002448.2 D31883.2

UniGene Cluster ID
438236

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss12077191	CEPH		184	AF					0.830	0.170

ss24125023	AFD_EUR_PANEL	European	48	IG	0.417	0.458	0.125	1.000	0.646	0.354

	AFD_AFR_PANEL	African American	46	IG	0.783	0.130	0.087	0.020	0.848	0.152

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.542	0.125	0.527	0.604	0.396

ss4989122	JBIC-allele		1308	AF					0.618	0.382

ss52067714	HapMap-CEU	European	120	IG	0.283	0.517	0.200		0.542	0.458

	HapMap-HCB	Asian	90	IG	0.622	0.200	0.178		0.722	0.278

	HapMap-JPT	Asian	90	IG	0.422	0.400	0.178		0.622	0.378

	HapMap-YRI	Sub-Saharan African	118	IG	0.780	0.220			0.890	0.110

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.423+/-0.181	332	260	9	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 .