Reference SNP(refSNP) Cluster Report: rs424306

Reference SNP(refSNP) Cluster Report: rs424306

refSNP ID: rs424306
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	80/129
Map to Genome Build:	36.3

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

HGVS Names
NM_007118.2:c.157+44328A>G
NT_006576.15:g.14178319A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1800625 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs424306 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
ss560918	SC_JCM\|AC010419.3_41556	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	07/12/00	10/10/03	80	Genomic	unknown
ss876230	KWOK\|OVLP-000804-30161	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	09/01/00	10/10/03	86	Genomic	99 %
ss879274	KWOK\|OVLP-000804-47141	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	09/01/00	10/10/03	86	Genomic	99 %
ss879944	KWOK\|OVLP-000804-49793	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	09/01/00	10/10/03	86	Genomic	99 %
ss880440	KWOK\|OVLP-000804-51951	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	09/01/00	10/10/03	86	Genomic	99 %
ss882524	KWOK\|OVLP-000804-60924	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	09/01/00	10/10/03	86	Genomic	99 %
ss1047612	KWOK\|OVLP-000804-12370	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	09/02/00	10/10/03	86	Genomic	96 %
ss1800625	KWOK\|OVLP-000925-637332	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	10/05/00	10/25/06	89	Genomic	99 %
ss1800983	KWOK\|OVLP-000925-642385	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	10/05/00	10/10/03	89	Genomic	99 %
ss1801461	KWOK\|OVLP-000925-647650	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	10/05/00	10/10/03	89	Genomic	99 %
ss1802065	KWOK\|OVLP-000925-653012	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	10/05/00	10/10/03	89	Genomic	99 %
ss1803133	KWOK\|OVLP-000925-659272	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	10/05/00	10/10/03	89	Genomic	99 %
ss1848626	KWOK\|OVLP-000925-658444	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	10/06/00	10/10/03	89	Genomic	96 %
ss6476840	WI_SSAHASNP\|NT_006576.11_10539477	fwd/T	A/G	ttgttggagttctgggctgaatattttgtg	tgtggttttcaagtgatcttagaataatta	02/12/03	10/10/03	111	Genomic	unknown

Fasta sequence (Legend)

 TCCTTGCCAG CCGAGGAGTT AGACTAGAAC ACCTTCAAGA TGAGCTGTAA CTTTTGAATA
 GTGAACACAG ATTTTATAAT ATCTGCTGGT GTTTTATTTG TCACATCTGC CAGTTTACCT
 AAAATTAAAA TTTTGAAAAC CATTTTTTGT GGAAAGGACA AATCATGTAC TTGTTGGAGT
 TCTGGGCTGA ATATTTTGTG
 R
 TGTGGTTTTC AAGTGATCTT AGAATAATTA TGATGCCAGC TAACTGTCCT TGAGTGCCAA
 TGCTGCCATG TATTGTTCTC ATTGCCTGTA TTATTTAATA AGTGtaatat tttctccatt
 ttacagatga ggaaactgag gtacagagag attggttaag tagcccaaag tacagagtta
 gttaagggat ggggtggttt gaacctagtt cttggcccat tctcttaacc acttcgctat
 aactgtTGTT AACTAAATCA TATAGTAGAC ATGAGTATAA TTTAACACAA TTTGTCTTTT
 ATATGACTGA TGAAATTAGC CCCGTGGGTT TATTTTCAAT GCCTTA

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	14178319	forward	intron

Celera	NW_922518->NM_007118->NP_009049	13315089	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs424306 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	6435931	14159833	plus	A	alt_assembly_8	HuRef	HuRef	view	200
5	NW_922518.1	13315089	14212657	plus	A	alt_assembly_1	Celera	Celera	view	200
5	NT_006576.15	14178319	14241319	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AC010419.4 AC013637 AC013637.3 AC016655.5 AC018548.10 AC020778.4 AC026456.3 AC027344.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC010419.6 AC016655.6 AC026456.5 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	A/A	A/G	HWP	A	G
ss1800625	HapMap-CEU	European	118	IG	1.000			1.000

	HapMap-HCB	Asian	86	IG	0.814	0.186	0.527	0.907	0.093

	HapMap-JPT	Asian	86	IG	0.930	0.070	1.000	0.965	0.035

	HapMap-YRI	Sub-Saharan African	120	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.052+/-0.153	270	210	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 .