Reference SNP(refSNP) Cluster Report: rs2853669

Reference SNP(refSNP) Cluster Report: rs2853669

refSNP ID: rs2853669
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NT_006576.15:g.1285349A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44657495 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2853669 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
ss1343109	TSC-CSHL\|TSC0190226	fwd/B	C/T	ttcgcgggcacagacgcccaggaccgcgct	cccacgtggcggagggactggggacccggg	06/14/01	10/10/03	108	Genomic	unknown
ss4040335	SC_JCM\|AY007685.1_24197	fwd/B	C/T	ttcgcgggcacagacgcccaggaccgcgct	cccacgtggcggagggactggggacccggg	09/26/01	10/10/03	100	Genomic	unknown
ss10212500	BCM_SSAHASNP\|chr5.NT_023089.13_1278087	rev/T	A/G	cccgggtccccagtccctccgccacgtggg	agcgcggtcctgggcgtctgtgcccgcgaa	06/27/03	10/10/03	116	Genomic	unknown
ss44657495	ABI\|hCV8773290	rev/T	A/G	cccgggtccccagtccctccgccacgtggg	agcgcggtcctgggcgtctgtgcccgcgaa	07/19/05	07/19/05	126	Genomic	unknown
ss48297101	SNP500CANCER\|TERT-67	fwd/B	C/T	ttcgcgrgcacagacgcccaggaccgcgct	cccacgtggcggagggactggggacccggg	08/19/05	11/03/06	126	Genomic	unknown
ss49784092	EGP_SNPS\|TERT-001620	fwd/B	C/T	ttcgcgggcacagacgcccaggaccgcgct	cccacgtggcggagggactggggacccggg	10/28/05	11/03/06	126	Genomic	unknown

Fasta sequence (Legend)

 CGTCCGGACC TGGAGGCAGC CCTGGGTCTC CGGATCAGGC CAGCGGCCAA AGGGTCGCCG
 CACGCACCTG TTCCCAGGGC CTCCACATCA TGGCCCCTCC CTCGGGTTAC CCCACAGCCT
 AGGCCGATTC GACCTCTCTC CGCTGGGGCC CTCGCTGGCG TCCCTGCACC CTGGGAGCGC
 GAGCGGCGCG CGGGCGGGGA AGCGCGGCCC AGACCCCCGG GTCCGCCCGG AGCAGCTGCG
 CTGTCGGGGC CAGGCCGGGC TCCCAGTGGA TTCGCGGGCA CAGACGCCCA GGACCGCGCT
 Y
 CCCACGTGGC GGAGGGACTG GGGACCCGGG CACCCGTCCT GCCCCTTCAC CTTCCAGCTC
 CGCCTCCTCC GCGCGGACCC CGCCCCGTCC CGACCCCTCC CGGGTCCCCG GCCCAGCCCC
 CTCCGGGCCC TCCCAGCCCC TCCCCTTCCT TTCCGCGGCC CCGCCCTCTC CTCGCGGCGC
 GAGTTTCAGG CAGCGCTGCG TCCTGCTGCG CACGTGGGAA GCCCTGGCCC CGGCCACCCC
 CGCGATGCCG CGCGCTCCCC GCTGCCGAGC CGTGCGCTCC CTGCTGCGCA GCCACTACCG

GeneView

GeneView via analysis of contig annotation: TERT telomerase reverse transcriptase

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_198253

function

reference

NT_006576->NM_198255

function

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


reference	NT_006576->NM_198253->NP_937983	1285349	reverse	5' near gene

reference	NT_006576->NM_198255->NP_937986	1285349	reverse	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2853669 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_001838923.2	847255	1275716	plus	T	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922518.1	434716	1332284	minus	G	alt_assembly_1	Celera	Celera	view	300
5	NT_006576.15	1285349	1348349	minus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023089 AF114847 AF121948 AF128893

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss48297101	P1		184	AF	0.120	0.326	0.554	0.100	0.283	0.717

	CAUC1		52	AF	0.115	0.385	0.500	0.655	0.308	0.692

	AFR1		48	AF		0.083	0.917	1.000	0.042	0.958

	HISP1		40	AF		0.450	0.550	0.200	0.225	0.775

	PAC1		44	AF	0.364	0.409	0.227	0.439	0.568	0.432

ss49784092	EGP_YORUB-PANEL	Sub-Saharan African	24	AF			1.000			1.000

	EGP_HISP-PANEL	Hispanic	44	AF		0.455	0.545	0.200	0.227	0.773

	EGP_CEPH-PANEL	European	44	AF	0.045	0.682	0.273	0.050	0.386	0.614

	EGP_AD-PANEL	African American	30	AF		0.267	0.733	0.584	0.133	0.867

	EGP_ASIAN-PANEL	Asian	48	AF	0.083	0.417	0.500	1.000	0.292	0.708

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.392+/-0.206	95	95	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 .