Reference SNP(refSNP) Cluster Report: rs26285

Reference SNP(refSNP) Cluster Report: rs26285

refSNP ID: rs26285
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
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
NM_007118.2:c.157+20920T>C
NT_006576.15:g.14154911T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44608183 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs26285 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
ss34360	KWOK\|OVLP-26961	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	04/28/00	04/07/04	76	Genomic	99 %
ss35256	KWOK\|OVLP-29015	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	04/28/00	10/10/03	76	Genomic	99 %
ss442613	KWOK\|OVLP-000621-355970	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	06/30/00	10/10/03	79	Genomic	99 %
ss444418	KWOK\|OVLP-000621-360486	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	06/30/00	10/10/03	79	Genomic	99 %
ss446369	KWOK\|OVLP-000621-365584	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	06/30/00	10/10/03	79	Genomic	99 %
ss447348	KWOK\|OVLP-000621-368513	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	06/30/00	10/10/03	79	Genomic	99 %
ss615456	SC_JCM\|AC010419.3_18029	fwd/B	C/T	agttactcttgcccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	07/12/00	10/10/03	80	Genomic	unknown
ss872418	KWOK\|OVLP-000804-12340	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	09/01/00	10/10/03	86	Genomic	99 %
ss873169	KWOK\|OVLP-000804-15681	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	09/01/00	10/10/03	86	Genomic	99 %
ss875528	KWOK\|OVLP-000804-26899	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	09/01/00	10/10/03	86	Genomic	99 %
ss876214	KWOK\|OVLP-000804-30138	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	09/01/00	10/10/03	86	Genomic	99 %
ss876644	KWOK\|OVLP-000804-32731	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	09/01/00	10/10/03	86	Genomic	99 %
ss879080	KWOK\|OVLP-000804-46171	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	09/01/00	10/10/03	86	Genomic	99 %
ss879921	KWOK\|OVLP-000804-49758	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	09/01/00	10/10/03	86	Genomic	99 %
ss881703	KWOK\|OVLP-000804-57299	fwd/B	C/T	agttactcttgcccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	09/01/00	10/10/03	86	Genomic	99 %
ss883056	KWOK\|OVLP-000804-62617	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	09/01/00	10/10/03	86	Genomic	99 %
ss884748	KWOK\|OVLP-000804-70881	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	09/01/00	10/10/03	86	Genomic	99 %
ss887114	KWOK\|OVLP-000804-84052	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	09/01/00	10/10/03	86	Genomic	99 %
ss1800501	KWOK\|OVLP-000925-636511	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	10/05/00	10/10/03	89	Genomic	99 %
ss1800660	KWOK\|OVLP-000925-638278	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	10/05/00	10/10/03	89	Genomic	99 %
ss1800806	KWOK\|OVLP-000925-640212	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	10/05/00	10/10/03	89	Genomic	99 %
ss1801344	KWOK\|OVLP-000925-646166	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	10/05/00	10/10/03	89	Genomic	99 %
ss1801673	KWOK\|OVLP-000925-649364	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	10/05/00	10/10/03	89	Genomic	99 %
ss1801792	KWOK\|OVLP-000925-650354	rev/T	A/G	ctgaattggacttagacatgcagatactcc	atgatgaaatccctctggcaagagtaactg	10/05/00	10/10/03	89	Genomic	99 %
ss1802042	KWOK\|OVLP-000925-652977	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	10/05/00	10/10/03	89	Genomic	99 %
ss1802987	KWOK\|OVLP-000925-658414	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	10/05/00	10/10/03	89	Genomic	99 %
ss1803117	KWOK\|OVLP-000925-659249	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	10/05/00	10/10/03	89	Genomic	99 %
ss17091981	CSHL-HAPMAP\|CSHL-HuAA-200402.chr5.NT_023089.13_14147649	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	02/17/04	03/04/04	120	Genomic	unknown
ss23984547	PERLEGEN\|afd3127169	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	08/10/04	09/13/04	123	Genomic	unknown
ss44608183	ABI\|hCV2999092	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	07/19/05	03/31/08	126	Genomic	unknown
ss76823909	AFFY\|AFFY_6_1M_SNP_A-8685341	rev/T	A/G	gacatgcagatactcc	atgatgaaatccctct	08/28/07	08/30/07	129	Genomic	unknown
ss93000645	BCMHGSC_JDW\|JWB-1939202	fwd/B	C/T	cagttactcttgccagagggatttcatcat	ggagtatctgcatgtctaagtccaattcag	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 GATGGTAGTA TTTGTTCAAG AATCCGATTT TCATTGAGGG CACAAAGGCT CTGTTGTGCC
 ACGCTCAGGA TCTTGTTTTC CTGAGATTGC TTCAGGCAGA TTTAAACAAT GGCCTCTCAA
 CGTACTGGAT TTAAAGAGTA AGTAGTTCTC CATGATCTTA TTTCTCATTA GTAGGGAAAT
 GTAAACTTTT ACCTTTGGTC AAAATTTTGC TCCTGTCACC TGACCCCCTG ATGTCATTAT
 GATTGTCTTT TCCTTGCAGT ATTGCCTTGT CAGTTACTCT TGCCAGAGGG ATTTCATCAT
 Y
 GGAGTATCTG CATGTCTAAG TCCAATTCAG CTCTTTACAT ATAGGCCCCA TGCCCTAAGT
 GTTGCTGTCA TTTTGCCTGT TTAGTTACTT TACAAACACT AATGGCACGT AAGGCTCCTG
 GGAACCCTGG GTCTGGAACA GGCACAGGCC ACAGAACAGA TGGCCCTTGC CAGGTGGTCC
 TTGGGTGCAC AGTGGCTGTG GAGCTGCTGT CTCTCAACAA AGGAAGGAAG GGCACTCTCA
 GGGAAATCAA ATGGATCAAA GCCGTCCCCT TACCCATGTT GCCCCTTTAA GCCTTCCCAG

GeneView

GeneView via analysis of contig annotation: TRIO triple functional domain (PTPRF interacting)

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_006576->NM_007118

function

Celera

NW_922518->NM_007118

function

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


reference	NT_006576->NM_007118->NP_009049	14154911	forward	intron

Celera	NW_922518->NM_007118->NP_009049	13291689	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs26285 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838927.1	6412522	14136424	plus	T	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922518.1	13291689	14189257	plus	T	alt_assembly_1	Celera	Celera	view	300
5	NT_006576.15	14154911	14217911	plus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023089 AC013637 AC013637.3 AC016655.5 AC018548.10 AC020778.4 AC027344 AC027344.2 AC074142.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC010419.6 AC016655.6 AC074142.3 NC_000005.8	AC013637.3 AC018548.12 AC020778.4 AC027344.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23984547	AFD_EUR_PANEL	European	48	IG	0.042	0.500	0.458	0.317	0.292	0.708

	AFD_AFR_PANEL	African American	44	IG	0.182	0.409	0.409	0.527	0.386	0.614

	AFD_CHN_PANEL	Asian	48	IG	0.208	0.583	0.208	0.439	0.500	0.500

ss34360	C		60	AF					0.700	0.300

	B		60	AF					0.250	0.750

	A		60	AF					0.400	0.600

ss44608183	HapMap-CEU	European	120	IG	0.483	0.417	0.100		0.692	0.308

	HapMap-HCB	Asian	90	IG	0.133	0.689	0.178		0.478	0.522

	HapMap-JPT	Asian	90	IG	0.356	0.378	0.267		0.544	0.456

	HapMap-YRI	Sub-Saharan African	120	IG	0.433	0.450	0.117		0.658	0.342

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.495+/-0.052	332	260	9	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 .