Reference SNP(refSNP) Cluster Report: rs1286735

Reference SNP(refSNP) Cluster Report: rs1286735

refSNP ID: rs1286735
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
Map to Genome Build:	36.3

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

HGVS Names
NM_000965.2:c.609+2492T>A
NM_016152.2:c.273+2492T>A
NT_022517.17:g.25553905T>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2026483 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1286735 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
ss2026483	KWOK\|OVLP-000925-645112	fwd/B	A/T	attcttttattccttatgaggactctgtga	ttgggtttcgttgccctcatattacagatg	10/06/00	04/07/04	87	Genomic	99 %
ss2370547	TSC-CSHL\|TSC0400935	fwd/B	A/T	attcttttattccttatgaggactctgtga	ttgggtttcgttgccctcatattacagatg	10/20/00	10/10/03	88	Genomic	95 %
ss2570327	SC_JCM\|AC074287.2_21375	rev/T	A/T	catctgtaatatgagggcaacgaaacccaa	tcacagagtccgcataaggaataaaagaat	11/03/00	10/10/03	92	Genomic	unknown
ss5839042	SC_JCM\|NT_005762.12_767870	fwd/B	A/T	attcttttattccttatgaggactctgtga	ttgggtttcgttgccctcatattacagatg	01/10/03	10/10/03	111	Genomic	unknown
ss17763258	CSHL-HAPMAP\|CSHL-HuCC-200402.chr3.NT_022517.16_25553866	fwd/B	A/T	attcttttattccttatgaggactctgtga	ttgggtttcgttgccctcatattacagatg	02/19/04	03/04/04	120	Genomic	unknown
ss42086911	ABI\|hCV8063634	fwd/	A/T	attcttttattccttatgaggactctgtga	ttgggtttcgttgccctcatattacagatg	07/17/05	07/17/05	126	Genomic	unknown
ss65721784	ILLUMINA\|Human1-rs1286735	fwd/B	A/T	attcttttattccttatgaggactctgtga	ttgggtttcgttgccctcatattacagatg	10/10/06	10/10/06	127	Genomic	unknown
ss84787062	HGSV\|Cor19240_SNV_20070510.chr3_25588905	fwd/	A/T	attcttttattccttatgaggactctgtga	ttgggtttcgttgccctcatattacagatg	11/30/07	12/08/07	130	Genomic	unknown

Fasta sequence (Legend)

 AGGGGCGAAA AGAGAAGATG AGAGAAAACA GGTGCTGTGC AATGGTGGAC TGTGTTGAGT
 TGAGAGCAAG TGGGAAGTGA GAATGGGAAA AGCCTGGCGG AGTCTTGAGT GCCACTTGAG
 GAGTCTGTAA ATAATGAACA GTAATTGATG GTTGTGGTCA AAAATCTTTA TTATTATCAT
 TGTAATCATT ATTACATCTC atatttattg agcatttact atgtactagg gaccatgcta
 agtactataa gtatactaat tcttttattc cttatgagga ctctgtga
 W
 ttgggtttcg ttgccctcat attacagatg caaaagccag gtacagaaag gctcgataac
 tttccccttg tctcttagtc aacaagtggt cagaggtgag acttgaacct aaacagtctg
 actccagggc agctctttta accagtatac tatacACAGA ATCCCTTGAG AGGGTTGCCA
 AAAAGGGAGA ATGGAAGCTG GGGCCATTGG CGGCATCTAG CTAGGAGGAG AGAGCTGTGA
 CCCAGGAATA AATCAATCTT GTAGCTCCAA GAAAGTCAGA GGAAAAGAGA TGAGAGTGGG
 GAGGTCTTCC TGAAAGAGGA GACTTTTGAT CCAGGTCATG AGGTGAGCGA CTTTA

GeneView

GeneView via analysis of contig annotation: RARB retinoic acid receptor, beta

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_022517->NM_000965

function

reference

NT_022517->NM_016152

function

HuRef

NW_001838877->NM_000965

function

HuRef

NW_001838877->NM_016152

function

Celera

NW_921651->NM_000965

function

Celera

NW_921651->NM_016152

function

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


reference	NT_022517->NM_000965->NP_000956	25553905	forward	intron

reference	NT_022517->NM_016152->NP_057236	25553905	forward	intron

HuRef	NW_001838877->NM_000965->NP_000956	40708285	reverse	intron

HuRef	NW_001838877->NM_016152->NP_057236	40708285	reverse	intron

Celera	NW_921651->NM_000965->NP_000956	25550779	forward	intron

Celera	NW_921651->NM_016152->NP_057236	25550779	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1286735 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_921651.1	25550779	25550779	plus	T	alt_assembly_1	Celera	Celera	view	288
3	NW_001838877.2	40708285	25559377	minus	A	alt_assembly_8	HuRef	HuRef	view	288
3	NT_022517.17	25553905	25588905	plus	T	ref_assembly	reference	reference	view	288

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022517 AC012037 AC074287.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss2026483	HapMap-CEU	European	116	IG	0.259	0.466	0.276	0.655	0.491	0.509

	HapMap-HCB	Asian	90	IG	0.133	0.556	0.311	0.273	0.411	0.589

	HapMap-JPT	Asian	88	IG	0.159	0.318	0.523	0.100	0.318	0.682

	HapMap-YRI	Sub-Saharan African	118	IG	0.237	0.542	0.220		0.508	0.492

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.493+/-0.058	270	210	0	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 .