Reference SNP(refSNP) Cluster Report: rs696125

Reference SNP(refSNP) Cluster Report: rs696125

refSNP ID: rs696125
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_001465.3:c.1135+2861T>C
NM_199335.2:c.1135+2861T>C
NT_006576.15:g.39171824A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5358920 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs696125 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
ss1153568	KWOK\|OVLP-000804-472134	fwd/B	C/T	tgtgacataaccaaatcatatatctgaggc	aaaatccaagtcttcagattgcaagtttaa	09/02/00	10/10/03	86	Genomic	99 %
ss1264836	KWOK\|OVLP-000804-470101	fwd/B	C/T	tgtgacataaccaaatcatatatctgaggc	aaaatccaagtcttcagattgcaagtttaa	09/02/00	10/10/03	86	Genomic	96 %
ss1264881	KWOK\|OVLP-000804-479119	rev/T	A/G	ttaaacttgcaatctgaagacttggatttt	gcctcagatatatgatttggttatgtcaca	09/02/00	10/10/03	86	Genomic	96 %
ss1427405	TSC-CSHL\|TSC0288284	fwd/B	C/T	tgtgacataaccaaatcatatatctgaggc	aaaatccaagtcttcagattgcaagtttaa	06/14/01	10/10/03	110	Genomic	unknown
ss1861247	KWOK\|OVLP-000925-4767	fwd/B	C/T	tgtgacataaccaaatcatatatctgaggc	aaaatccaagtcttcagattgcaagtttaa	10/06/00	10/10/03	87	Genomic	99 %
ss2462719	SC_JCM\|AC007914.2_11866	rev/T	A/G	ttaaacttgcaatctgaagacttggatttt	gcctcagatatatgatttggttatgtcaca	11/03/00	10/10/03	92	Genomic	unknown
ss5308782	TSC-CSHL\|TSC1637104	fwd/B	C/T	tgtgacataaccaaatcatatatctgaggc	aaaatccaagtcttcagattgcaagtttaa	09/20/02	10/10/03	110	Genomic	unknown
ss5358920	TSC-CSHL\|TSC1524749	fwd/B	C/T	tgtgacataaccaaatcatatatctgaggc	aaaatccaagtcttcagattgcaagtttaa	09/20/02	10/25/06	110	Genomic	unknown
ss23433323	PERLEGEN\|afd3110944	rev/T	A/G	ttaaacttgcaatctgaagacttggatttt	gcctcagatatatgatttggttatgtcaca	08/10/04	09/13/04	123	Genomic	unknown
ss44611136	ABI\|hCV7510113	rev/T	A/G	ttaaacttgcaatctgaagacttggatttt	gcctcagatatatgatttggttatgtcaca	07/19/05	07/19/05	126	Genomic	unknown
ss76684225	AFFY\|AFFY_6_1M_SNP_A-8545576	fwd/B	C/T	atcatatatctgaggc	aaaatccaagtcttca	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 CAAAAGCGTT CTTTTGCAAC AATACTGCAG AAAATAAACT CGTGTATGTG TCATAAAGTA
 AGCATTTATT TTCTGAACAC AAAGTTTTTT AAGTCAGGTC TGCTGACTCT TGATCCTGCC
 ACTGCTATTT TTCTTAAACA ATGCTAGAAA TACTAAGTAA TTTACCATTT CATTTAGGAA
 GGTTAAAATA TATCAGAATT AGAAAGTATA TGTTCATTTT ATATAACTGG ATAAGCAATA
 TAAAGAAAAG AATTAAATTT CTGTTGTAGC AAAATTTTTT AAAATTCTGA AATTCTATTT
 TTTATAATTC TGGAGTATGT AAGTAGaaaa taaataatta ttaaataatt aaataataat
 atacatatac gtatacataa acatGTGGTA TATTGTACGT ACAGTCTTTA GATGGGAAAA
 TTCTTTATTA AGTGTAATTA TCGCCCCCAT TTCACAAATG AGTGTTGAGA TGTGACATAA
 CCAAATCATA TATCTGAGGC
 Y
 AAAATCCAAG TCTTCAGATT GCAAGTTTAA TACTTTCTCC ATGTACCATC GTGCCCCtgt
 atgtatgttt gcatgtttat gtttaaagca taagtgtatt atttatttat atagaatata
 tatgcagata ttccttgact tgtgatcggg ttacatcctt ataaacattc ttaagttgga
 aatattataa actgaaaaca cgtttaatat acctaactac caaatgtcat agcttagcct
 agcccacctt aaacatgctc tgaacactta cattagccta caattgggca aaatcatctc
 acacaaagcc tattttataa taaagtgttg actatctcat gtaatttatt gaatactgta
 ccatggtttc tactgaatgc atattgcttt tgtaccatca taaagtcaag taatcattaa
 tttgaactgt cataaatagg gcaccatctg tgtatgtata catattatta ctaatatgta
 catgGGATTT TAACTTTTTT

GeneView

GeneView via analysis of contig annotation: FYB FYN binding protein (FYB-120/130)

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_001465

function

reference

NT_006576->NM_199335

function

HuRef

NW_001838933->NM_001465

function

HuRef

NW_001838933->NM_199335

function

Celera

NW_922596->NM_001465

function

Celera

NW_922596->NM_199335

function

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


reference	NT_006576->NM_001465->NP_001456	39171824	reverse	intron

reference	NT_006576->NM_199335->NP_955367	39171824	reverse	intron

HuRef	NW_001838933->NM_001465->NP_001456	3493266	reverse	intron

HuRef	NW_001838933->NM_199335->NP_955367	3493266	reverse	intron

Celera	NW_922596->NM_001465->NP_001456	4796138	reverse	intron

Celera	NW_922596->NM_199335->NP_955367	4796138	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs696125 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_922596.1	4796138	39085624	minus	A	alt_assembly_1	Celera	Celera	view	500
5	NW_001838933.1	3493266	39150655	minus	A	alt_assembly_8	HuRef	HuRef	view	500
5	NT_006576.15	39171824	39234824	minus	A	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000005.5 AC015575 AC015575.5 AC025471.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC010633.8 AC025471.6 NC_000005.8	AC007914.2 AC015575.5

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23433323	AFD_EUR_PANEL	European	48	IG			1.000			1.000

	AFD_AFR_PANEL	African American	46	IG	0.043	0.261	0.696	0.752	0.174	0.826

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.250	0.708	0.655	0.167	0.833

ss5358920	CEPH		184	AF						1.000

	HapMap-CEU	European	120	IG		0.067	0.933	1.000	0.033	0.967

	HapMap-HCB	Asian	90	IG	0.022	0.222	0.756	1.000	0.133	0.867

	HapMap-JPT	Asian	90	IG		0.156	0.844		0.078	0.922

	HapMap-YRI	Sub-Saharan African	120	IG	0.050	0.300	0.650	0.655	0.200	0.800

	CHMJ	Asian	74	IG					0.135	0.865

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.199+/-0.245	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 .