Reference SNP(refSNP) Cluster Report: rs2836253

Reference SNP(refSNP) Cluster Report: rs2836253

refSNP ID: rs2836253
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002243.3:c.-117+4616C>T
NM_170736.1:c.-117+4616C>T
NT_011512.10:g.25295593C>T
XM_497783.2:c.552+10609G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10990711 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2836253 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
ss4016139	PERLEGEN\|P00224054	fwd/B	C/T	aaagaacgttatgctagttgtgccactaga	cctagaatggtattgaatgcatgaataata	09/26/01	04/07/04	100	Genomic	unknown
ss10990711	BCM_SSAHASNP\|chr21.NT_011512.8_25294118	fwd/B	C/T	aaagaacgttatgctagttgtgccactaga	cctagaatggtattgaatgcatgaataata	06/30/03	10/25/06	116	Genomic	unknown
ss23802913	PERLEGEN\|afd0080204	fwd/B	C/T	aaagaacgttatgctagttgtgccactaga	cctagaatggtattgaatgcatgaataata	08/10/04	09/13/04	123	Genomic	unknown
ss67679267	ILLUMINA\|HumanHap650Yv1.0_rs2836253	fwd/B	C/T	aaagaacgttatgctagttgtgccactaga	cctagaatggtattgaatgcatgaataata	11/14/06	11/14/06	127	Genomic	unknown
ss71329330	ILLUMINA\|HumanHap650Yv3.0_rs2836253	fwd/B	C/T	aaagaacgttatgctagttgtgccactaga	cctagaatggtattgaatgcatgaataata	04/23/07	04/23/07	127	Genomic	unknown
ss75352240	ILLUMINA\|ILMN_Human_1M_rs2836253	fwd/B	C/T	aaagaacgttatgctagttgtgccactaga	cctagaatggtattgaatgcatgaataata	08/28/07	08/29/07	129	Genomic	unknown
ss78852610	HGSV\|Cor18507_SNV_20070510.chr21_38555593	fwd/B	C/T	aaagaacgttatgctagttgtgccactaga	cctagaatggtattgaatgcatgaataata	10/19/07	10/21/07	129	Genomic	unknown

Fasta sequence (Legend)

 ATTGGCACCT TGCCATGAAA GGTAGGTCCT TGTACTGTAG TTGAACCTTT AGGTCATATC
 TCAGCTCAAG GGTAAGATGC TATCAAAGCT GCTTTTCCTA TGGTAGAATA TGTGAGTACT
 GAAATTAACT GTGCGCTTTT TCCACCTGAA AAGCCCCCAA CTTAAAACCT AAAGAACGTT
 ATGCTAGTTG TGCCACTAGA
 Y
 CCTAGAATGG TATTGAATGC ATGAATAATA AGCATCTTCC TGAGCAGACT TGAGGGCTTG
 CCCCAGTGGA ATATCTGTGT CTTTGGTGAG AAGCCTTCCT CTTTTTTCCT TAGTTTCTAT
 TAACGCTGTT TCCAATTTTC AATAGCAGTT AATTGTGTCA TTTCTTGGTA GAAATGCTGG
 CTAAACCCAT GCCTACCAAG

GeneView

GeneView via analysis of contig annotation: LOC441964 hypothetical LOC441964

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: KCNJ15 potassium inwardly-rectifying channel, subfamily J, member 15

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_011512->XM_497783

function

Celera

NW_927384->XM_941458

function

reference

NT_011512->NM_002243

function

reference

NT_011512->NM_170736

function

HuRef

NW_001838708->NM_002243

function

HuRef

NW_001838708->NM_170736

function

Celera

NW_927384->NM_002243

function

Celera

NW_927384->NM_170736

function

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


reference	NT_011512->XM_497783->XP_497783	25295593	reverse	intron

Celera	NW_927384->XM_941458->XP_946551	24316703	reverse	intron

reference	NT_011512->NM_002243->NP_002234	25295593	forward	intron

reference	NT_011512->NM_170736->NP_733932	25295593	forward	intron

HuRef	NW_001838708->NM_002243->NP_002234	653153	reverse	intron

HuRef	NW_001838708->NM_170736->NP_733932	653153	reverse	intron

Celera	NW_927384->NM_002243->NP_002234	24316703	forward	intron

Celera	NW_927384->NM_170736->NP_733932	24316703	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2836253 maps exactly once on NCBI human chromosome 21

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
21	NW_927384.1	24316703	24831580	plus	C	alt_assembly_1	Celera	Celera	view	200
21	NW_001838708.2	653153	25103191	minus	G	alt_assembly_8	HuRef	HuRef	view	200
21	NT_011512.10	25295593	38555593	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011512

dbSNP Blast Analysis
GenBank HTGS Finished:
AP000162.1 AP001434.1 NC_000021.7

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10990711	HapMap-CEU	European	120	IG	0.650	0.333	0.017	0.403	0.817	0.183

	HapMap-HCB	Asian	90	IG	0.222	0.489	0.289	1.000	0.467	0.533

	HapMap-JPT	Asian	90	IG	0.133	0.622	0.244		0.444	0.556

	HapMap-YRI	Sub-Saharan African	120	IG	0.283	0.467	0.250	0.655	0.517	0.483

ss23802913	AFD_EUR_PANEL	European	48	IG	0.792	0.208		0.584	0.896	0.104

	AFD_AFR_PANEL	African American	46	IG	0.261	0.435	0.304	0.584	0.478	0.522

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.583	0.333	0.251	0.375	0.625

ss4016139	NCBI\|NIHPDR		20	AF					0.600	0.400

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.488+/-0.077	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .