Reference SNP(refSNP) Cluster Report: rs6460945

Reference SNP(refSNP) Cluster Report: rs6460945

refSNP ID: rs6460945
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:	Not available
Clinical Association:	unknown

HGVS Names
NM_017802.3:c.2431+2088G>A
NT_007819.16:g.310828G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43037720 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6460945 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
ss10406234	BCM_SSAHASNP\|chr7.NT_007819.13_117457	fwd/T	A/G	tcttcctggcgtggccgcctcccgtcgcgc	gcgtcagaaactcggatcttcgtggcgtgg	06/29/03	10/10/03	116	Genomic	unknown
ss11263896	SC_JCM\|chr7.NT_007819.13_117457	fwd/T	A/G	tcttcctggcgtggccgcctcccgtcgcgc	gcgtcagaaactcggatcttcgtggcgtgg	07/03/03	10/10/03	116	Genomic	unknown
ss43037720	ABI\|hCV29083441	fwd/T	A/G	tcttcctggcgtggccgcctcccgtcgcgc	gcgtcagaaactcggctcttcgtggcgtgg	07/18/05	07/18/05	126	Genomic	unknown
ss93611150	BCMHGSC_JDW\|JWB-2258478	fwd/T	A/G	tcttcctggcgtggccgcctcccgtcgcgc	gcgtcagaaactcggatcttcgcggcgtgg	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 TACCCGCGGG CTGTCCCTGC GGCTGTACTC TGCTCATTCT TCCCTTTGCT GTGTGGAAGC
 TTTGGGCCTG GATGTGCTGA CTTTGCCTTT TGCCTCCTTT GGAAAATACT TAGACCTTCC
 CCGCGCAGCT GCGTCCGGTT TCCCGGCGTG GCTACATCCG GTTATGCGAT GTCGGATCTT
 CCTGGTGTGG CCGCCTCCCG TCGCGCAGCG TCAGAAACTC GGATCTTCGT GGCGTGGCCG
 CCTCCCGACA CGCGGCGTCA GAAACTCGGA TCTTCCTGGC GTGGCCGCCT CCCGTCGCGC
 R
 GCGTCAGAAA CTCGGCTCTT CGTGGCGTGG CCGCCTCCCG ACACGCGGCG TCAGAAACTC
 GCATCTTCCC GGCGTGGCCG CCTCCCGTCA CGCGGCGTCA GAAACTCGCA TCTTCCCGGC
 GTGGCCGCCT CCCGTCACGC GGCGTCAGAA ACTCGCATCT TCCTGGTGTG GCCGCCTCCC
 GTCACGCGGC GTCAGAAACT CGGATCTTCC CGGCGTGGCC GCGTCCCGTC ACGCGGCGTC
 AGAAACTCGC ATCTTCCTGG TGTGGCCGCC TCCCGTCACG CGGCGTCAGA AACTCGGATC

GeneView

GeneView via analysis of contig annotation: LOC100134488 hypothetical protein LOC100134488

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: HEATR2 HEAT repeat containing 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

CRA_TCAGchr7v2

NT_079592->XM_001722307

function

reference

NT_007819->NM_017802

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


CRA_TCAGchr7v2	NT_079592->XM_001722307->XP_001722359	830143	forward	517	synonymous	G	Ala [A]	3	46
					contig reference	A	Ala [A]	3	46

reference	NT_007819->NM_017802->NP_060272	310828	forward		intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6460945 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001838998.1	542428	740183	plus	A	alt_assembly_8	HuRef	HuRef	view	300
7	NT_007819.16	310828	788395	plus	G	ref_assembly	reference	reference	view	300
7	NW_923206.1	733111	790714	plus	G	alt_assembly_1	Celera	Celera	view	300
7	NT_079592.2	830143	880143	plus	A	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007819

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank mRNA:
XM_001125899.1	AK127690.1

Population Diversity

There is no frequency data.

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 .