Reference SNP(refSNP) Cluster Report: rs3011288

Reference SNP(refSNP) Cluster Report: rs3011288

refSNP ID: rs3011288
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	101/129
Map to Genome Build:	36.3

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

HGVS Names
NM_012087.2:c.374-495G>C
NT_035014.4:g.2695560G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss94181681 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3011288 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
ss4237454	SC_JCM\|AL593851.5_183454	fwd/T	C/G	tcaccaaagagggctgttcttttgggacaa	gtttcccaagtgattcataaaacataacac	10/15/01	10/10/03	101	Genomic	unknown
ss12947702	SC_SNP\|NT_035014.3_2695560	fwd/T	C/G	tcaccaaagagggctgttcttttgggacaa	gtttcccaagtgattcataaaacataacac	10/21/03	10/31/03	119	Genomic	unknown
ss94181681	BCMHGSC_JDW\|JWB-2656752	fwd/	C/G	tcaccaaagagggctgttcttttgggacaa	gtttcccaagtgattcataaaacataacac	02/26/08	03/06/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGGCCCACAG GAGGTGCCTG GCATATTACT AACAAGGCTT AGAGATGGCT AAGTTACATC
 TGCAGTTCTA GGCAGAATCT GAAGAGTATA AAGATTGAGA AGGGCAAAGA GGACTAGAAA
 GAAAAGAGGG GAAGAAGAAA GTGAAATGAA GGAGAAGCAG GACCTGGGGT CCCATGGGTT
 GGGCATTTTT AATGGCAGTC ATTCTGGTGG GTCATGGCAT TCACCAAAGA GGGCTGTTCT
 TTTGGGACAA
 S
 GTTTCCCAAG TGATTCATAA AACATAACAC CTCATATTTT TCATCGAATT GAACCAGCAT
 CTTGCTGCTC TGTGTGTGTC TCTGGACTGG CAGCATCAGC CTCACCTGGG AGCTTGGTAG
 AAATGCACCA GGTCAGAACC TGCATTTAGC AAGATCCCAG CAGATTCATA TGCATGTTAC
 TAGGTTGGTG CAAAGGTAAT TGCAGGTTTT ACAGTTAAAA GTAACATTCA TCTAAGAAGC
 ACTGACCTGG

GeneView

GeneView via analysis of contig annotation: GTF3C5 general transcription factor IIIC, polypeptide 5, 63kDa

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_035014->NM_012087

function

HuRef

NW_001839241->NM_012087

function

Celera

NW_924573->NM_012087

function

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


reference	NT_035014->NM_012087->NP_036219	2695560	forward	intron

HuRef	NW_001839241->NM_012087->NP_036219	541692	reverse	intron

Celera	NW_924573->NM_012087->NP_036219	19948181	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3011288 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839241.2	541692	105412322	minus	C	alt_assembly_8	HuRef	HuRef	view	200
9	NW_924573.1	19948181	106460350	plus	G	alt_assembly_1	Celera	Celera	view	200
9	NT_035014.4	2695560	134908441	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_035014 AC000394 AL162417

dbSNP Blast Analysis
GenBank HTGS Finished:
AL162417.23

Population Diversity

There is no frequency data.

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 .