Reference SNP(refSNP) Cluster Report: rs3936177

Reference SNP(refSNP) Cluster Report: rs3936177

refSNP ID: rs3936177
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:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_015456.2:c.1239-45G>A
NT_024000.16:g.944650G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5194227 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3936177 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
ss5194227	TSC-CSHL\|TSC0032601	fwd/B	C/T	ccatcagccccacctcagccccacctcagc	ccacaccgacccctgcccagccctgaggca	09/20/02	10/10/03	108	Genomic	unknown
ss13498343	WI_SSAHASNP\|chr9.NT_078081.2_16070	fwd/B	C/T	acctcagccccacctcagccccacctcagc	ccacaccgacccctgcccagccctgaggca	10/31/03	11/10/03	126	Genomic	unknown
ss13531992	SC_JCM\|chr9.NT_078081.2_16070	fwd/B	C/T	acctcagccccacctcagccccacctcagc	ccacaccgacccctgcccagccctgaggca	10/31/03	11/07/03	126	Genomic	unknown
ss22871235	SSAHASNP\|WGSA-200403-chr9.chr9.NT_078081.2_16070	fwd/B	C/T	acctcagccccacctcagccccacctcagc	ccacaccgacccctgcccagccctgaggca	03/21/04	03/22/04	126	Genomic	unknown

Fasta sequence (Legend)

 CCGCAGGGAA GACACAGCCA GGCACCGCCC GTCAGGACTT ACCCAGCCCG GGCAGCAGGC
 GGAGGAGCGC GTTCTTGTTC CTCTGCTTGG TGATGTGCAG GACGTAGTAC AGCCCCACCT
 CGCAGGCCAT GCGCTGCTCC TGCAGAAACC TGCGCCCGGG GCGCCATCAG CCCCACCTCA
 GCCCCACCTC AGC
 Y
 CCACACCGAC CCCTGCCCAG CCCTGAGGCA GCCCCCTGGG CAACAGTGCC ATCCCTGCGC
 CACGGCCACC CCTGCACCAT GGCCCTACAG CCCGTACTTA GTGAAGCTTT CGGGAAGTGT
 GTTTGGATAT GAGACTGGGG CTTTCTCCTC AGCCGGAAGT TTCTGATCCA CATTGAAAGT
 GTAGTCATCC ACCAGGAAGG ACATGAGCAT CGGGAGGAAC CTGGTGATGA GCTCTACCTC
 CTACGAGGAG GGGAGGCCAT GAGCGGGCGC GGGCCCGGGC CCTGCCCCAC CCCACCCTGA
 CATGACACAC ACCCTGCCCC TGGCCCTCCC ACTCCCCCAG ATACCTAACC GACCCTCCCT
 GCTATTCAGG TCCCCAGGTC CCTCTTCCCA CCTCCCGAGT CCCCCACCCA GGCCATCTCC
 TCAAACCCCT TTGGGTCTGG ACCCCCTGAG GGTCACCACC T

GeneView

GeneView via analysis of contig annotation: COBRA1 cofactor of BRCA1

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_024000->NM_015456

function

HuRef

NW_001839245->NM_015456

function

Celera

NW_924573->NM_015456

function

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


reference	NT_024000->NM_015456->NP_056271	944650	forward	intron

HuRef	NW_001839245->NM_015456->NP_056271	957750	forward	intron

Celera	NW_924573->NM_015456->NP_056271	24165272	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3936177 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_001839245.1	957750	109620939	minus	A	alt_assembly_8	HuRef	HuRef	view	193
9	NW_924573.1	24165272	110677441	minus	A	alt_assembly_1	Celera	Celera	view	193
9	NT_024000.16	944650	139281468	minus	G	ref_assembly	reference	reference	view	193

NCBI Resource Links

Submitter-Referenced
GenBank
NT_078081

dbSNP Blast Analysis
GenBank HTGS Finished:
BX255925.17 NC_000009.10

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .