Reference SNP(refSNP) Cluster Report: rs1055975

Reference SNP(refSNP) Cluster Report: rs1055975

refSNP ID: rs1055975
Organism:	human (Homo sapiens)
Molecule Type:	cDNA
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_004772.1:c.*28T>C
NT_034772.5:g.13481603A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24787308 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1055975 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
ss1535261	LEE\|647674	fwd/B	C/T	taatcgtaacacctccatttgtattacata	ggtgtatgggtattgatgaggtcatggtat	09/13/00	10/10/03	86	cDNA	unknown
ss4321349	CGAP-GAI\|245494	rev/T	A/G	ataccatgacctcatcaatacccatacacc	tatgtaatacaaatggaggtgttacgatta	11/28/01	10/10/03	102	cDNA	unknown
ss4423752	LEE\|e647674	fwd/B	C/T	taatcgtaacacctccatttgtattacata	ggtgtatgggtattgatgaggtcatggtat	04/26/02	10/10/03	106	cDNA	unknown
ss16261270	CGAP-GAI\|1522800	fwd/B	C/T	taatcgtaacacctccatttgtattacata	ggtgtatgggtattgatgaggtcatggtat	11/18/03	11/22/03	120	cDNA	unknown
ss24787308	SEQUENOM\|sqnm72904	rev/T	A/G	ataccatgacctcatcaatacccatacacc	tatgtaatacaaatggaggtgttacgatta	06/18/04	11/02/06	124	cDNA	unknown
ss93207568	BCMHGSC_JDW\|JWB-2021722	rev/T	A/G	ataccatgacctcatcaatacccatacacc	tatgtaatacaaatggaggtgttacgatta	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 CGCTGCCTCC CTGACTCCAC TGGNCAGCAG TGAACTCCGC TCCCCAAGAA TCAGTTACCT
 CCACTTTTTT TAATCGTAAC ACCTCCATTT GTATTACATA
 Y
 GGTGTATGGG TATTGATGAG GTCATGGTAT CATATATGGG ATTTTTTTCT GTGTAAATCA
 TCAAGTATAA GAAGAAACTA TGGGACTCTG AGCCTTGCTT

GeneView

GeneView via analysis of contig annotation: C5orf13 chromosome 5 open reading frame 13

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_034772->NM_004772

function

HuRef

NW_001838952->NM_004772

function

Celera

NW_922751->NM_004772

function

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


reference	NT_034772->NM_004772->	13481603	reverse	416	3' UTR

HuRef	NW_001838952->NM_004772->	27731488	forward	390	3' UTR

Celera	NW_922751->NM_004772->	11633355	reverse	416	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1055975 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_001838952.2	27731488	106245220	plus	T	alt_assembly_8	HuRef	HuRef	view	100
5	NW_922751.1	11633355	107012184	minus	A	alt_assembly_1	Celera	Celera	view	100
5	NT_034772.5	13481603	111094489	minus	A	ref_assembly	reference	reference	view	100
7	NT_079592.2	23522447	23572447	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	100

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
CGAP-C-24549 sqnm72904	AA211306 BE552319 Hs.142827

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank STS:	GenBank mRNA:
NM_004772.1	AC022108.4 NC_000005.8	AC026229.3 AC109995.1	BV174587.1 BV174588.1	AF119859.1 BC011050.1 BC019068.2 BC072013.1 BC072443.1 U30521.1

UniGene Cluster ID
483067

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	C	T
ss24787308	CEPH		184	AF		0.070	0.930

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.130+/-0.219	0	0	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 .