Reference SNP(refSNP) Cluster Report: rs12004998

Reference SNP(refSNP) Cluster Report: rs12004998

refSNP ID: rs12004998
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
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_005157.3:c.549+348G>A
NM_007313.2:c.606+348G>A
NT_035014.4:g.507771G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43724984 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12004998 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
ss18020133	CSHL-HAPMAP\|CSHL-HuCC-200402.chr9.NT_035014.3_507771	fwd/T	A/G	tattttataatgatagaaatcatccccaac	agaaaaattcaaataatagataacctttct	02/19/04	03/04/04	120	Genomic	unknown
ss43724984	ABI\|hCV2605125	fwd/T	A/G	tattttataatgatagaaatcatccccaac	agaaaaattcaaataatagataacctttct	07/18/05	11/03/06	126	Genomic	unknown
ss46564738	EGP_SNPS\|ABL1-143573	fwd/T	A/G	tattttataatgatagaaatcatccccaac	agaaaaattcaaataatagataacctttct	08/03/05	11/03/06	126	Genomic	unknown

Fasta sequence (Legend)

 CCAGAGGTCC TGCTGTCGGA TTGATAAATT ATTGCAAGAA AGCTCAACCA AGAAGATGTT
 TAAAGAATCT TTCAGGTGGG AGTCATTCCA TTAGCCTTAT GAAGACCCTT TATTGAGGAT
 CCGTTCTGTG ATATTACAAG TTCCTGGGAC TGGTATGATT CTCTTATTGT CTTGCTAGAG
 TTTTGTTGTT AGCAAGTTAC TTAAAATAGG AGGAATATCT GTTGGGTTTT GGACACATTT
 TTTACAATAA GATTCTTCCT TTAAAAAAAA TATTTTATAA TGATAGAAAT CATCCCCAAC
 R
 AGAAAAATTC AAATAATAGA TAACCTTTCT TAGAGCGAAA GACCACTTTA CTATCCCCTC
 CCCCACAGAC GCCTGGCACG TGGGCTTCTT CCTGCGGATG AACACATTCA TGGAGAGGTG
 TGTGGACATA CGTGCATACA CGCATGCAGT TTTCAGTGAA AACCGGGATC AAACCCACAG
 CTTACCAAAC CCAAAGTGTG GTGTTGTAAG GGAGGTGGCC TATATGATTT TGTGGTCTTC
 ATATAAATAA TCCTTAAGAG TCCATAAAGA GAAGGGAGGA GTTAACATTG ACTGAGGTAT

GeneView

GeneView via analysis of contig annotation: ABL1 c-abl oncogene 1, receptor tyrosine kinase

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_035014->NM_005157

function

reference

NT_035014->NM_007313

function

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


reference	NT_035014->NM_005157->NP_005148	507771	forward	intron

reference	NT_035014->NM_007313->NP_009297	507771	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12004998 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839240.1	509371	103216668	plus	G	alt_assembly_8	HuRef	HuRef	view	300
9	NW_924573.1	17756946	104269115	plus	G	alt_assembly_1	Celera	Celera	view	300
9	NT_035014.4	507771	132720652	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_035014

dbSNP Blast Analysis
GenBank HTGS Finished:
AL161733.20

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss43724984	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	90	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.183	0.817	0.439	0.092	0.908

ss46564738	EGP_YORUB-PANEL	Sub-Saharan African	24	AF	0.250	0.750	0.655	0.125	0.875

	EGP_HISP-PANEL	Hispanic	44	AF	0.045	0.955	1.000	0.023	0.977

	EGP_CEPH-PANEL	European	44	AF		1.000			1.000

	EGP_AD-PANEL	African American	30	AF	0.267	0.733	0.584	0.133	0.867

	EGP_ASIAN-PANEL	Asian	48	AF		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.060+/-0.163	307	247	58	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .