Reference SNP(refSNP) Cluster Report: rs547914

Reference SNP(refSNP) Cluster Report: rs547914

refSNP ID: rs547914
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_004980.3:c.1107-49683T>C
NM_172198.1:c.1107-49683T>C
NT_019273.18:g.8287096A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1886170 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs547914 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
ss718796	SC_JCM\|AL357144.4_16198	fwd/B	C/T	ccacaggccttagactcagaggtgggatct	gggaaatttacccaacatctgtcaacctgt	07/27/00	10/10/03	83	Genomic	unknown
ss1082956	KWOK\|OVLP-000804-82037	fwd/B	C/T	ccacaggccttagactcagaggtgggatct	gggaaatttacccaacatctgtcaacctgt	09/02/00	10/10/03	123	Genomic	99 %
ss1886170	KWOK\|OVLP-000925-254904	fwd/B	C/T	ccacaggccttagactcagaggtgggatct	gggaaatttacccaacatctgtcaacctgt	10/06/00	10/25/06	123	Genomic	99 %
ss13020537	SC_SNP\|NT_019273.15_2817225	rev/T	A/G	acaggttgacagatgttgggtaaatttccc	agatcccacctctgagtctaaggcctgtgg	10/22/03	10/31/03	123	Genomic	unknown
ss14425978	WUGSC_SSAHASNP\|chr1.NT_019273.16_3375359	rev/T	A/G	acaggttgacagatgttgggtaaatttccc	agatcccacctctgagtctaaggcctgtgg	11/05/03	11/22/03	123	Genomic	unknown
ss23219954	PERLEGEN\|afd1089101	rev/T	A/G	acaggttgacagatgttgggtaaatttccc	agatcccacctctgagtctaaggcctgtgg	08/10/04	09/13/04	123	Genomic	unknown
ss76468125	AFFY\|AFFY_6_1M_SNP_A-8329109	rev/T	A/G	gttgggtaaatttccc	agatcccacctctgag	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 CATGATGATA CTGCAGAGAA AAGACTGGGC CTGGGAACTG TTACATCAGA GGGCAGAGTG
 AGGGCTAGCA GGGGAGTGAC AGTCTTGGTC ATTAATTCAC TGAGACCCTA AGTATGTCCC
 TAAGCCTGTC TGGATCTTTG CTCCTTTATC TTCAAAATAC AGATAAGGAC ACTTTTTGGT
 CAGTTTTATA GGGTGACTGA GAGGATAAAA TGACTTAATA CATATGGAAA TGCACTGAAT
 GAAAGACACT GTGGTTAATA AACATATGTT GGTATTAAAA CTAACTTAAA TGTTGATTTC
 CTTTTGTGTC AATTCACAGG GGGTGGGGAA AAGTACAAGA CACTCTTACT AGAAATGCTT
 ACTTTATTTA AACTGGAAAG CCACCAGGGA CAAGTGAAGG GTACCGGGGA TGGAGTTTGG
 AATCCTGAAC TCATAGAGAA GTCAAGGCCA GACTGGAGAG AATCCACAGG CCTTAGACTC
 AGAGGTGGGA TCT
 Y
 GGGAAATTTA CCCAACATCT GTCAACCTGT TTCTGAGCCA TAAAATGGCT CAGGGGTCGC
 TGGGGGTCTA TTTGCATGAA CAGGTTAGCA CTCAGCAAGC TCCTTATAAT CTGCCCCTCT
 GGAAGCTATG AGGAAATGGT GGTGATCCTA ATACCGCTAC CCACAGGGTC TGTCAGGTGA
 GATGGTCACT GCCCTTGGAG GCTTCTGGAG GTCAGAAGAG AAAAAGCCCA CCCTCACAGG
 AAACAAAC

GeneView

GeneView via analysis of contig annotation: KCND3 potassium voltage-gated channel, Shal-related subfamily, member 3

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_019273->NM_004980

function

reference

NT_019273->NM_172198

function

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


reference	NT_019273->NM_004980->NP_004971	8287096	reverse	intron

reference	NT_019273->NM_172198->NP_751948	8287096	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs547914 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838594.1	3500113	110250807	minus	A	alt_assembly_8	HuRef	HuRef	view	493
1	NW_922462.1	3344222	110626011	minus	A	alt_assembly_1	Celera	Celera	view	493
1	NT_019273.18	8287096	112180934	minus	A	ref_assembly	reference	reference	view	493

NCBI Resource Links

Submitter-Referenced
GenBank
NT_019273 AC022181 AL357144.10 AL357144.7

dbSNP Blast Analysis
GenBank HTGS Finished:
AL450997.5

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1886170	HapMap-CEU	European	120	IG	0.017	0.400	0.583	0.200	0.217	0.783

	HapMap-HCB	Asian	88	IG	0.045	0.364	0.591	1.000	0.227	0.773

	HapMap-JPT	Asian	88	IG	0.023	0.250	0.727	1.000	0.148	0.852

	HapMap-YRI	Sub-Saharan African	116	IG	0.069	0.397	0.534	1.000	0.267	0.733

ss23219954	AFD_EUR_PANEL	European	48	IG	0.042	0.250	0.708	0.655	0.167	0.833

	AFD_AFR_PANEL	African American	46	IG	0.217	0.391	0.391	0.371	0.413	0.587

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.333	0.583	0.655	0.250	0.750

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.357+/-0.226	332	260	9	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 .