Reference SNP(refSNP) Cluster Report: rs4134896

Reference SNP(refSNP) Cluster Report: rs4134896

refSNP ID: rs4134896
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
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_005641.2:c.-59-1010G>A
NM_139122.1:c.-59-1010G>A
NM_139123.1:c.-59-1010G>A
NM_139315.1:c.-59-1010G>A
NT_007933.14:g.24947177C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss85474424 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4134896 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
ss5587117	EGP_SNPS\|TAF2E-005177	fwd/T	A/G	aaggaaagctgagcctgggccagacacttc	gctcacgcctttaattccaacactttgaga	09/27/02	04/07/04	108	Genomic	unknown
ss75123248	ILLUMINA\|ILMN_Human_1M_rs4134896	fwd/T	A/G	aaggaaagctgagcctgggccagacacttc	gctcacgcctttaattccaacactttgaga	08/28/07	08/29/07	129	Genomic	unknown
ss85474424	HGSV\|Cor18517_SNV_20070510.chr7_99357552	rev/B	C/T	tctcaaagtgttggaattaaaggcgtgagc	gaagtgtctggcccaggctcagctttcctt	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 GGATGGTCTC CATCTCTTGA CCTGGTGATC CGTCCGCCTC GGCCTCCCAA AGTGCTGGGA
 TTACAGGTGT GAGCCAACGC GCCCGACCGG ATTTATTTTT TTACCTTTTT TTTTTTTTTG
 AGACAGAGTC CATCTGTCAC TGAGGCTGGA GTGCAATGGC GCAATCTCAA CTCACTGCAA
 ACTCTACTGC CGAGGCTCAA GTGATTCTCC TGCCTCAGCC TCCCAAGTAG CTGGGATTAC
 AGGCACGCGC CACCATGCCC AGCTAATTTT TGTATTTTTA GTAGAGAAAG GGTTTTACCA
 TGTTGCTCAG GCTGGTCTCG AACTCCTGAC CTGAAGTGAT CCACCCACCT TGGCCTCCCA
 AATTGCTGGA ATTACAGACG TGAGCCACCG CACCTGGCCT ACCTGGTGGA TTTGATGTGA
 AGGCTCAGAT AAAGAACAAG TGTCTGGATG GATGGCATTG CTATGAAGAT AAGGAAAGCT
 GAGCCTGGGC CAGACACTTC
 R
 GCTCACGCCT TTAATTCCAA CACTTTGAGA GGCCAACGCT GGAGGATTGC TTGAGCCCAA
 AACTTCAAAG TGGTGGGATT GAAGCCCTGA GGTGTAACAG AAAAAGATAA AAATCTGGGC
 TGGGCCTGGT GGCTCAGGCC TGTAATTCCA ACACTTTGGG AGGCCGAAGC AGGAGGACTG
 CGTGAGCCCA GCAGTTCAAG ACCAGCCTGG ACAACATAGT GAGACTCTGT CTCTGCCCCT
 GCCCCTGCAA AAAATTGGCT GTGTGTAGTG GTACACACCT ATAGTCCCAG CTACTTGGGA
 GGCTGAGGTG TGAGGATTGC TTGAGCCTAG GAGCTCCTGG GCTCTATCAG TTTTCCCACC
 TCTGCCTCCT GAGTAGCTAG AACAACAGCC CTGTGCCTGC ATACCCAGCT AATTTTTGTA
 TTTTTTGTAC AGATGGGGTC TCACTGTGTT GTCCAGGCTG GTCGTGAACT GCTGGGCTCA
 AGCGATCCTC CTACCTTGGG

GeneView

GeneView via analysis of contig annotation: TAF6 TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa

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_007933->NM_005641

function

reference

NT_007933->NM_139122

function

reference

NT_007933->NM_139123

function

reference

NT_007933->NM_139315

function

HuRef

NW_001839065->NM_005641

function

HuRef

NW_001839065->NM_139122

function

HuRef

NW_001839065->NM_139123

function

HuRef

NW_001839065->NM_139315

function

Celera

NW_923574->NM_005641

function

Celera

NW_923574->NM_139122

function

Celera

NW_923574->NM_139123

function

Celera

NW_923574->NM_139315

function

CRA_TCAGchr7v2

NT_079595->NM_005641

function

CRA_TCAGchr7v2

NT_079595->NM_139122

function

CRA_TCAGchr7v2

NT_079595->NM_139123

function

CRA_TCAGchr7v2

NT_079595->NM_139315

function

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


reference	NT_007933->NM_005641->NP_005632	24947177	reverse	intron

reference	NT_007933->NM_139122->NP_620834	24947177	reverse	intron

reference	NT_007933->NM_139123->NP_620835	24947177	reverse	intron

reference	NT_007933->NM_139315->NP_647476	24947177	reverse	intron

HuRef	NW_001839065->NM_005641->NP_005632	806708	forward	intron

HuRef	NW_001839065->NM_139122->NP_620834	806708	forward	intron

HuRef	NW_001839065->NM_139123->NP_620835	806708	forward	intron

HuRef	NW_001839065->NM_139315->NP_647476	806708	forward	intron

Celera	NW_923574->NM_005641->NP_005632	22986598	reverse	intron

Celera	NW_923574->NM_139122->NP_620834	22986598	reverse	intron

Celera	NW_923574->NM_139123->NP_620835	22986598	reverse	intron

Celera	NW_923574->NM_139315->NP_647476	22986598	reverse	intron

CRA_TCAGchr7v2	NT_079595->NM_005641->NP_005632	24974232	reverse	intron

CRA_TCAGchr7v2	NT_079595->NM_139122->NP_620834	24974232	reverse	intron

CRA_TCAGchr7v2	NT_079595->NM_139123->NP_620835	24974232	reverse	intron

CRA_TCAGchr7v2	NT_079595->NM_139315->NP_647476	24974232	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4134896 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839065.2	806708	94348536	plus	G	alt_assembly_8	HuRef	HuRef	view	255
7	NW_923574.1	22986598	94447561	minus	C	alt_assembly_1	Celera	Celera	view	255
7	NT_079595.2	24974232	99073020	minus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	255
7	NT_007933.14	24947177	99550837	minus	C	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY149894

dbSNP Blast Analysis
GenBank HTGS Finished:
AC073842.5 NC_000007.12

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss5587117	PDR90	Global	178	IG	0.067	0.933	0.752	0.034	0.966

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.065+/-0.168	90	90	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .