Reference SNP(refSNP) Cluster Report: rs1713419

Reference SNP(refSNP) Cluster Report: rs1713419

refSNP ID: rs1713419
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/129
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
NT_026437.11:g.1834388A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss89869197 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1713419 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
ss2549659	SC_JCM\|AC068147.2_13422	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	11/03/00	04/07/04	89	Genomic	unknown
ss4934357	YUSUKE\|IMS-JST100079	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	08/01/02	10/10/03	108	Genomic	unknown
ss10731491	BCM_SSAHASNP\|chr14.NT_026437.10_754676	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	06/30/03	10/10/03	116	Genomic	unknown
ss21170063	SSAHASNP\|WGSA-200403-chr14.chr14.NT_026437.10_754676	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	03/19/04	03/19/04	121	Genomic	unknown
ss66577638	ILLUMINA\|HumanHap300v1.1_rs1713419	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	11/09/06	11/09/06	127	Genomic	unknown
ss67178444	ILLUMINA\|HumanHap550v1.1_rs1713419	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	11/14/06	11/14/06	127	Genomic	unknown
ss67541775	ILLUMINA\|HumanHap650Yv1.0_rs1713419	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	11/14/06	11/14/06	127	Genomic	unknown
ss69149847	PERLEGEN\|PGP09648320	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	01/30/07	08/14/07	127	Genomic	unknown
ss70450851	ILLUMINA\|HumanHap300v2.0_rs1713419	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	04/18/07	11/18/07	127	Genomic	unknown
ss70656468	ILLUMINA\|HumanHap550v3.0__rs1713419	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	04/20/07	03/30/08	130	Genomic	unknown
ss71216467	ILLUMINA\|HumanHap650Yv3.0_rs1713419	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	04/23/07	04/23/07	127	Genomic	unknown
ss74893960	ILLUMINA\|ILMN_Human_1M_rs1713419	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	08/28/07	08/29/07	129	Genomic	unknown
ss79729736	HGSV\|Cor18507_SNV_20070510.chr14_19904388	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	11/23/07	11/23/07	130	Genomic	unknown
ss83864688	KRIBB_YJKIM\|KHS560264	fwd/B	C/T	ataatccttgccagaaatcctgcagcgaac	atggcatggcatcatcctagtcattgattt	12/04/07	12/05/07	130	Genomic	unknown
ss85210956	HGSV\|Cor19129_SNV_20070510.chr14_19904388	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	12/06/07	12/08/07	130	Genomic	unknown
ss89869197	BCMHGSC_JDW\|JWB-0744115	rev/T	A/G	aaatcaatgactaggatgatgccatgccat	gttcgctgcaggatttctggcaaggattat	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCCAGGTTTT ACATGGAGAA ATAACCTGAG GGACTTTATT TCTATCCAAT GCCCTGGTTT
 CCATCCTGAC CAGAGGATGA TGACATCCGC TGATAGGCCA TGCTTCTGTC TTCTCTTATG
 TGCCTCATGC CAAGCCTCGA AATATACCTT CTGGACCATC ATTTCCACAT CTACCTTGTG
 ACTAGAAGTC CTAGTTATGG TATTTTGAAA TTTATGATCC ATAATCCTTG CCAGAAATCC
 TGCAGCGAAC
 Y
 ATGGCATGGC ATCATCCTAG TCATTGATTT CAATCTTTTG CCTTTTGCTC CCCTAAAATC
 TTGGGCCAAT TGCAGGAGGA AGCTCTATTT GTCTCTCTTC CATGCTCTGA AAATTATATA
 AAAGCATCCC AGCTAAGGCT GGAGTGAAGG GGTTGGGGAA AGTTAAGCAA AGGCTAACTT
 GACCAATAGG CTCAATAGAT TCAGTCTTGT TGGCCAGGCC CACTTGAAGG GTTTTTTGTT
 TCATCTTGGA

GeneView

GeneView via analysis of contig annotation: TEP1 telomerase-associated protein 1

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_026437->NM_007110

function

HuRef

NW_001838110->NM_007110

function

Celera

NW_925539->NM_007110

function

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


reference	NT_026437->NM_007110->NP_009041	1834388	reverse	3' near gene

HuRef	NW_001838110->NM_007110->NP_009041	645235	reverse	3' near gene

Celera	NW_925539->NM_007110->NP_009041	637827	reverse	3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1713419 maps exactly once on NCBI human chromosome 14

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
14	NW_925539.1	637827	695705	minus	G	alt_assembly_1	Celera	Celera	view	200
14	NW_001838110.1	645235	956411	minus	G	alt_assembly_8	HuRef	HuRef	view	200
14	NT_026437.11	1834388	19904388	minus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_026437 AL355075

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL355075.6 NC_000014.7	AC068147.2

UniGene Cluster ID
508835

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss2549659	CEPH		184	AF					0.490	0.510

	HapMap-CEU	European	120	IG	0.150	0.533	0.317	0.479	0.417	0.583

	HapMap-HCB	Asian	88	IG	0.159	0.523	0.318	0.584	0.420	0.580

	HapMap-JPT	Asian	88	IG	0.159	0.500	0.341	1.000	0.409	0.591

	HapMap-YRI	Sub-Saharan African	120	IG	0.517	0.383	0.100	0.584	0.708	0.292

ss4934357	JBIC-allele		1486	AF					0.328	0.672

ss69149847	HapMap-CEU	European	120	GF	0.150	0.533	0.317		0.417	0.583

	HapMap-HCB	Asian	90	GF	0.156	0.533	0.311		0.422	0.578

	HapMap-JPT	Asian	90	GF	0.156	0.489	0.356		0.400	0.600

	HapMap-YRI	Sub-Saharan African	120	GF	0.533	0.283	0.183		0.675	0.325

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss2549659	262	76	117	67
ss69149847	262

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs1713419	270	76	117	67

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5135	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5135	ss69149847	G/G	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	chr14-HapMap-YRI
5240	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5240	ss69149847	A/A	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	chr14-HapMap-YRI
5245	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5245	ss69149847	A/A	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	chr14-HapMap-YRI
5273	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA19101	YOR042.03	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5273	ss69149847	A/A	CSHL-HAPMAP	HapMap-YRI	NA19101	YOR042.03	chr14-HapMap-YRI
5295	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5295	ss69149847	A/A	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	chr14-HapMap-YRI
5300	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA19119	YOR060.03	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5300	ss69149847	A/A	CSHL-HAPMAP	HapMap-YRI	NA19119	YOR060.03	chr14-HapMap-YRI
5307	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5307	ss69149847	A/A	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	chr14-HapMap-YRI
5309	ss2549659	C/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	r23_ch14_YRI_illumina:golden_gate_1.1.0	839432
5309	ss69149847	A/A	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	chr14-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	270

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .