Reference SNP(refSNP) Cluster Report: rs764164

Reference SNP(refSNP) Cluster Report: rs764164

refSNP ID: rs764164
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002240.2:c.-27-18081G>C
NT_011512.10:g.24892962C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14437417 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs764164 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
ss150588	TSC-CSHL\|TSC0066534	fwd/B	C/G	aaattctccatgggttttttttgaagatat	ataaagggagctatagaaatataacttaag	09/06/00	04/07/04	86	Genomic	95 %
ss14437417	WUGSC_SSAHASNP\|chr21.NT_011512.9_24891488	fwd/B	C/G	aaattctccatgggttttttttgaagatat	ataaagggagctatagaaatataacttaag	11/05/03	04/07/04	119	Genomic	unknown
ss21828379	SSAHASNP\|WGSA-200403-chr21.chr21.NT_011512.9_24891488	fwd/B	C/G	aaattctccatgggttttttttgaagatat	ataaagggagctatagaaatataacttaag	03/20/04	03/20/04	121	Genomic	unknown
ss65951205	AFFY\|SNP_A-1740663	fwd/B	C/G	ctccatgggttttttttgaagatat	ataaagggagctatagaaatataac	10/26/06	10/26/06	127	Genomic	unknown
ss91837410	BCMHGSC_JDW\|JWB-1495731	fwd/	C/G	aaattctccatgggttttttttgaagatat	ataaagggagctatagaaatataacttaag	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 ggctgaggca ggagaatggc gtgaacccgg gaggcggagc ttgcagtgag ccgagatctg
 gccactgcac tccagcctgg gcgacagagc aagactccgt ctcaaaaaaa aaaaaaaaaa
 aaaaaaaaga aaGTTCAGAT TAAGCTCAAT TCTTAATATT GATAGAGCAT GCTAGGTCCT
 GGAGGGGAAA AGGGGATTCA TGGGcactga tatatatcct aatatagtta ctgcacttca
 gagaaaaaag aaataatttt acaggcatca aagcataaag ggcacataga aaaggggaaa
 aacagactat ctttagcctt ctctctagaa acattcaaca agacaatggg ataagatcta
 aagtctttgg gaaaataaag tgagatacta cagttttata ctcagccaca ctggtgttca
 agcaaagaaa tgcctgagag atatcttaaa gatgcaagca ctcaggaatg aaattctcca
 tgggtttttt ttgaagaTAT
 S
 ATAAAGGGAG CTATAGAAAT ATAACTTAAG GGAATAAAGG TCAGCACTAG ATGAACTAGG
 AATAACAGCG TAACCAATTA AAACCAGGCA GGGAAGGTGA AGGAGGAAAG AAACTACATG
 AAAATAGAAA ATCAAAGAAT CTCAATTTAA ACATACTTTA TGGTAGGGAG ACAAAAGTTT
 CTGTCTAAAG AACAAAGATG

GeneView

GeneView via analysis of contig annotation: KCNJ6 potassium inwardly-rectifying channel, subfamily J, member 6

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->NM_002240

function

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


reference	NT_011512->NM_002240->NP_002231	24892962	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs764164 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	23914780	24429657	plus	C	alt_assembly_1	Celera	Celera	view	500
21	NW_001838707.1	241988	24704264	plus	G	alt_assembly_8	HuRef	HuRef	view	500
21	NT_011512.10	24892962	38152962	plus	C	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011512 AP000014.2 AP000158.1 AP001433.1 AP001730.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AP000158.1 AP001433.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss14437417	HapMap-CEU	European	118	IG	0.153	0.559	0.288	0.294	0.432	0.568

	HapMap-HCB	Asian	90	IG	0.200	0.489	0.311	1.000	0.444	0.556

	HapMap-JPT	Asian	88	IG	0.136	0.500	0.364	0.752	0.386	0.614

	HapMap-YRI	Sub-Saharan African	120	IG	0.533	0.350	0.117	0.251	0.708	0.292

ss150588	AfAm	African American	12	IG	0.333	0.667		0.251	0.667	0.333

	Caucasian	European	22	IG	0.273	0.182	0.545	0.050	0.364	0.636

	Asian	Asian	12	IG		0.500	0.500	0.439	0.250	0.750

	CEPH	European	12	IG	0.333	0.667		0.251	0.667	0.333

	PDpanel	Global	48	IG	0.083	0.458	0.458	0.752	0.312	0.688

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.499+/-0.017	323	262	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .