Reference SNP(refSNP) Cluster Report: rs1344087

Reference SNP(refSNP) Cluster Report: rs1344087

refSNP ID: rs1344087
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NT_007758.11:g.1835583A>G
XM_001128828.2:c.226+5380A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss42921663 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1344087 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
ss2120974	TSC-CSHL\|TSC0068693	fwd/B	C/T	tatacttttgaagtgaaatagatgtttaga	tttcttgtacttaatcagatgctttgtgct	10/19/00	04/07/04	88	Genomic	95 %
ss5520786	TSC-CSHL\|TSC0590411	fwd/B	C/T	tatacttttgaagtgaaatagatgtttaga	tttcttgtacttaatcagatgctttgtgct	09/21/02	10/10/03	108	Genomic	unknown
ss5969604	SC_JCM\|NT_007758.8_1834048	rev/T	A/G	agcacaaagcatctgattaagtacaagaaa	tctaaacatctatttcacttcaaaagtata	01/10/03	10/10/03	111	Genomic	unknown
ss6502123	WI_SSAHASNP\|NT_007758.8_1834048	rev/T	A/G	agcacaaagcatctgattaagtacaagaaa	tctaaacatctatttcacttcaaaagtata	02/12/03	10/10/03	111	Genomic	unknown
ss10369971	BCM_SSAHASNP\|chr7.NT_007758.10_1835583	rev/T	A/G	agcacaaagcatctgattaagtacaagaaa	tctaaacatctatttcacttcaaaagtata	06/29/03	10/10/03	116	Genomic	unknown
ss14573178	WUGSC_SSAHASNP\|chr7.NT_007758.10_1835583	rev/T	A/G	agcacaaagcatctgattaagtacaagaaa	tctaaacatctatttcacttcaaaagtata	11/05/03	11/22/03	120	Genomic	unknown
ss42921663	ABI\|hCV26340153	rev/T	A/G	agcacaaagcatctgattaagtacaagaaa	tctaaacatctatttcacttcaaaagtata	07/18/05	11/03/06	126	Genomic	unknown
ss75312844	ILLUMINA\|ILMN_Human_1M_rs1344087	fwd/B	C/T	tatacttttgaagtgaaatagatgtttaga	tttcttgtacttaatcagatgctttgtgct	08/28/07	08/29/07	129	Genomic	unknown
ss79013013	HGSV\|Cor18507_SNV_20070510.chr7_63246890	rev/T	A/G	agcacaaagcatctgattaagtacaagaaa	tctaaacatctatttcacttcaaaagtata	10/19/07	10/21/07	129	Genomic	unknown

Fasta sequence (Legend)

 ACAAATCAGA AAGAAAAACA TATACATAAG ACACAGCCCT AGTAGTCTTC ATAGTAAAGA
 AGATAAAATT ATAAAATAAT AGTTATTAAG AAATAGGTAA CAATTTGGAA TTTATTATGT
 TTATTATGTG CTGGACAGTG TTCTAAGTAA CCTATGGTAT TAGTGTTTTT AGGAATTCTG
 TGAGGTGAGT AGATAAAATC AACTATTCCA CAGTAGAGGC AATTGTCATA TAGAATTTAA
 ATTTCTAAGT TTAGTTCCTA CTAAGAAAAA TATACTTTTG AAGTGAAATA GATGTTTAGA
 Y
 TTTCTTGTAC TTAATCAGAT GCTTTGTGCT CTGATAAAAG TTCTCACTTT CATTTTCTGT
 ATGATCAACT GATTGGAAAT TATAAAGCAG AAACATATGA CATCTGTTCC GGGCCTCTCT
 CAAATCTCTT AACCAAATCT CCCTACTCCT CTCTAACATA ATGCACAGAT TTTTAAAAAC
 ACCTCCAAAA ATTTGGACAA ATTTTCCAGA TCCCTCAAAG CAATAGAAGA GCAGTTAGAT
 TATTTAGATC CTTACAGCAT AAAAAGGAGT TGTCTCTCAC TGTGAATGCA CCAGCAGATT

GeneView

GeneView via analysis of contig annotation: LOC728927 similar to hCG40110

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_007758->XM_001128828

function

HuRef

NW_001839034->XM_001719655

function

Celera

NW_923306->XM_001128919

function

CRA_TCAGchr7v2

NT_079593->XM_001715174

function

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


reference	NT_007758->XM_001128828->XP_001128828	1835583	forward	intron

HuRef	NW_001839034->XM_001719655->XP_001719707	564344	forward	intron

Celera	NW_923306->XM_001128919->XP_001128919	526311	forward	intron

CRA_TCAGchr7v2	NT_079593->XM_001715174->XP_001715226	1835582	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1344087 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_923306.1	526311	57522372	minus	A	alt_assembly_1	Celera	Celera	view	300
7	NW_001839034.1	564344	60183483	minus	G	alt_assembly_8	HuRef	HuRef	view	300
7	NT_079593.2	1835582	63140334	minus	A	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	300
7	NT_007758.11	1835583	63440175	minus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007758.8

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss2120974	AfAm	African American	36	IG	0.333	0.444	0.222	0.752	0.556	0.444

	Caucasian	European	38	IG	0.053	0.526	0.421	0.343	0.316	0.684

	Asian	Asian	36	IG	0.056	0.389	0.556	1.000	0.250	0.750

	CEPH	European	36	IG	0.056	0.111	0.833	0.100	0.111	0.889

	PDpanel	Global	34	IG	0.176	0.235	0.588	0.100	0.294	0.706

ss42921663	HapMap-CEU	European	120	IG	0.067	0.400	0.533	1.000	0.267	0.733

	HapMap-HCB	Asian	84	IG	0.143	0.500	0.357	1.000	0.393	0.607

	HapMap-JPT	Asian	84	IG	0.119	0.524	0.357	0.479	0.381	0.619

	HapMap-YRI	Sub-Saharan African	112	IG	0.250	0.446	0.304	0.439	0.473	0.527

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.457+/-0.140	359	298	3	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .