Reference SNP(refSNP) Cluster Report: rs26288

Reference SNP(refSNP) Cluster Report: rs26288

refSNP ID: rs26288
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_007118.2:c.157+4987G>A
NT_006576.15:g.14138978G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44676255 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs26288 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
ss34325	KWOK\|OVLP-26889	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	04/28/00	10/10/03	76	Genomic	99 %
ss34393	KWOK\|OVLP-27009	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	04/28/00	10/10/03	76	Genomic	99 %
ss35265	KWOK\|OVLP-29032	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	04/28/00	10/10/03	76	Genomic	99 %
ss322627	KWOK\|OVLP-000621-28114	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	06/30/00	10/10/03	79	Genomic	99 %
ss442654	KWOK\|OVLP-000621-356021	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	06/30/00	10/10/03	79	Genomic	99 %
ss443846	KWOK\|OVLP-000621-358554	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	06/30/00	10/10/03	79	Genomic	99 %
ss615188	SC_JCM\|AC027344.2_89997	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	07/12/00	05/16/04	80	Genomic	unknown
ss872399	KWOK\|OVLP-000804-12316	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	09/01/00	10/10/03	86	Genomic	99 %
ss873208	KWOK\|OVLP-000804-15737	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	09/01/00	10/10/03	86	Genomic	99 %
ss876185	KWOK\|OVLP-000804-30100	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	09/01/00	10/10/03	86	Genomic	99 %
ss876685	KWOK\|OVLP-000804-32783	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	09/01/00	10/10/03	86	Genomic	99 %
ss879904	KWOK\|OVLP-000804-49734	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	09/01/00	10/10/03	86	Genomic	99 %
ss883039	KWOK\|OVLP-000804-62592	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	09/01/00	10/10/03	86	Genomic	99 %
ss1801285	KWOK\|OVLP-000925-646062	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	10/05/00	10/10/03	89	Genomic	99 %
ss1801665	KWOK\|OVLP-000925-649345	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	10/05/00	10/10/03	89	Genomic	99 %
ss1801784	KWOK\|OVLP-000925-650335	rev/B	C/T	cccttgctccagctggggacccagcctggt	cctgcagcccattaattaaaatgaggctga	10/05/00	10/10/03	89	Genomic	99 %
ss1802025	KWOK\|OVLP-000925-652953	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	10/05/00	10/10/03	89	Genomic	99 %
ss1802970	KWOK\|OVLP-000925-658392	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	10/05/00	10/10/03	89	Genomic	99 %
ss1803094	KWOK\|OVLP-000925-659222	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	10/05/00	10/10/03	89	Genomic	99 %
ss44676255	ABI\|hCV613801	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	07/19/05	07/19/05	126	Genomic	unknown
ss78261035	HGSV\|Cor12878_SNV_20070510.chr5_14201978	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	10/17/07	10/18/07	129	Genomic	unknown
ss78875289	HGSV\|Cor18507_SNV_20070510.chr5_14201978	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	10/19/07	10/21/07	129	Genomic	unknown
ss93000589	BCMHGSC_JDW\|JWB-1939176	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	02/26/08	03/03/08	129	Genomic	unknown
ss108825692	1000GENOMES\|CEU.trio.12.15.2008_1210209_chr5_14201978	fwd/T	A/G	tcagcctcattttaattaatgggctgcagg	accaggctgggtccccagctggagcaaggg	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 CCTCAATTCT ATAATGAATT GGCTTTTATT TCCTTAAGTG CATTGTCTTG ACAAAATTTT
 AACAGCGCCA CTGGCAGGAA ATAGTAGCGA CTCCCTGGAC AGTGAAGACT TGGATTTGCG
 GGAGAATCCC AGTGTATTCT GGTGGAAAGT GCGTGCTCTG ACCTCATCCT CCCATTTCTT
 CCAAGTACTC AGCTGCGTAG ACTTGGCCAA ACTGACAAGG GTGATGGTGT GGTTGGCCTG
 GTGGATGGAG ATGCTGTCTT TTGAATCTTC TCAGCCTCAT TTTAATTAAT GGGCTGCAGG
 R
 ACCAGGCTGG GTCCCCAGCT GGAGCAAGGG GTAAGCGGGT TCGATGTGCA TCCACAGGGT
 TCTCTTCGTC CTATTCCAGT TCTGCTGACG CGCTGTTCAG TGGGCCACTG GGAGAGGGAA
 TGAACAGGGA GACTTCCCAG TGACCCTTGC ACTTGGGAAT TCTGGCTGCT GTTACTCAGC
 GGGAGCTGTT CTGGGAATTC CTATTGCTGT GCCTCTGAAC TGAGGGGAAG GGAGCATAGA
 GGAGTGGTCA GAGGCTTGCG GGGCCCTGCA TGTGCTGCTG GCTTCCTGCT GGACCCCTGG

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

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


reference	NT_006576->NM_007118->NP_009049	14138978	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs26288 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	6396590	14120492	plus	G	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922518.1	13275723	14173291	plus	G	alt_assembly_1	Celera	Celera	view	300
5	NT_006576.15	14138978	14201978	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
AC027344 AC010419 AC013637 AC013637.3 AC016655.5 AC018548.10 AC027344.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss615188	CEPH		184	AF		0.330	0.670

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.442+/-0.160	0	0	0	0

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 .