Reference SNP(refSNP) Cluster Report: rs25946

Reference SNP(refSNP) Cluster Report: rs25946

refSNP ID: rs25946
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
Map to Genome Build:	36.3

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

HGVS Names
NM_054027.3:c.97-17764T>G
NT_006576.15:g.14777064A>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10236136 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs25946 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
ss30802	KWOK\|OVLP-12684	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	04/28/00	10/10/03	76	Genomic	99 %
ss32852	KWOK\|OVLP-23501	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	04/28/00	10/10/03	76	Genomic	99 %
ss337063	KWOK\|OVLP-000621-76770	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	06/30/00	10/10/03	79	Genomic	99 %
ss543030	SC_JCM\|AC026437.2_12049	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	07/12/00	10/10/03	80	Genomic	unknown
ss1117928	KWOK\|OVLP-000804-295746	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	09/02/00	10/10/03	86	Genomic	99 %
ss1119700	KWOK\|OVLP-000804-306490	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	09/02/00	10/10/03	86	Genomic	99 %
ss1120014	KWOK\|OVLP-000804-308339	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	09/02/00	10/10/03	86	Genomic	99 %
ss1790730	KWOK\|OVLP-000925-516851	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	10/05/00	10/10/03	89	Genomic	99 %
ss1791408	KWOK\|OVLP-000925-524121	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	10/05/00	10/10/03	89	Genomic	99 %
ss1791942	KWOK\|OVLP-000925-530255	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	10/05/00	10/10/03	89	Genomic	99 %
ss3432395	SC_JCM\|AC022496.15_53459	fwd/T	A/C	aaaataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	09/24/01	10/10/03	100	Genomic	unknown
ss10236136	BCM_SSAHASNP\|chr5.NT_023089.13_14769802	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	06/27/03	04/07/04	116	Genomic	unknown
ss22305256	SSAHASNP\|WGSA-200403-chr5.chr5.NT_023089.13_14769802	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	03/21/04	03/21/04	121	Genomic	unknown
ss42570328	ABI\|hCV3088135	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	07/18/05	07/18/05	126	Genomic	unknown
ss66452213	AFFY\|SNP_A-2220533	rev/B	G/T	ccttctgccctctgga	gaaccataattattta	10/29/06	08/14/07	127	Genomic	unknown
ss68928188	PERLEGEN\|PGP04550962	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	01/30/07	08/14/07	127	Genomic	unknown
ss75147034	ILLUMINA\|ILMN_Human_1M_rs25946	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	08/28/07	08/29/07	129	Genomic	unknown
ss76243476	AFFY\|AFFY_6_1M_SNP_A-2220533	rev/B	G/T	ccttctgccctctgga	gaaccataattattta	08/28/07	08/30/07	129	Genomic	unknown
ss83474680	HGSV\|Cor18956_SNV_20070510.chr5_14840064	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	11/30/07	12/05/07	130	Genomic	unknown
ss83941488	HGSV\|Cor19240_SNV_20070510.chr5_14840064	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	11/30/07	12/06/07	130	Genomic	unknown
ss85616172	HGSV\|Cor18517_SNV_20070510.chr5_14840064	fwd/T	A/C	aacataggaaaggttaaataattatggttc	tccagagggcagaaggtcacccaccaaaca	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 GAAATAAATT AAAGAAGTAG TTCCTAAATA AAgaaaacca cagcatttta ttaaagttca
 taaaatgaga cctgaataaa tggagaggca aactatgttc cttgatgaga agacataatg
 tcataaatat gtcagagctc tttctgaact catttgtaaa tctgatggcg ttccagtcag
 aattctagtg atctAGTGAT TTGCATTTTT ATTTGGACCT GGGCAAAATG AGTTTTAACT
 CCACATAGGA GAAAAAACAA GAGAAATGTG ATAGAGGAGA CTAGTGAGGG GCACTTGCCT
 TAGCAGATAT TTAACTACAG AGAAGCCGGC TCCCAGAAGA AGCAATGCTC ACAGGGCACA
 GACACATCAA AAGATGCTCT GCCTCAGCCA AAGTCAGAGA AAGAAAAACT GAAACAAGAT
 GGTTGTCAAA TTTTaaaaat taaaataaat ggtaaaacct agcgctagca aagacgaata
 atgggaaatg tcagatagta ttggtgggtg tgtaagctgc tataattgtg tggaaaagga
 atatatcaag aggtattata attaaaagtg tgacaactcc ttgacccagt aatccccctt
 cagaaatcca tctaaacaaa agccccagta cataatgaca tgtacaaata gatgttcatg
 aaagcgttct ttgtcatgac acacagctga taataatcca tgtgtccacc aacataggaa
 aggttaaata attatggtTC
 M
 TCCAGAGGGC AGAAGGTCAC CCACCAAACA TGAAGTGAAA GTCAATGTAC TGAAGTAGAA
 AGAGGCCCAA GAAACAggcc gggtgcggtg gctcacgcct gtaattccag cactttggaa
 ggctgaggca ggtggatcac ctgaggtcag gagttcaaga ccagcctaac caacatggtg
 aaaccccgtc tctactaaaa atacaaagat tagcctggcc tggttgcatg cgcctgtaat
 cccagctact tgggaagctg aggcaggaga attgcttgaa cctgggaggt ggaggttgca
 gtgagccaag atagcgccat tgcactccag cctgggcaac agagcaagac tccatctcaa
 aaaaagaaaa aaagaaaGAG GCCCAAGAAA CAGTGTTAAG TAGAAGTAAG TTGCAAGTCA
 AGCAATATAA AATATTCTCA TTCTGTTAAA AACATAAAAA AAGACCCTAA AAAATGTGTG
 AGTATATTTG TATGAGCAGA GATAT

GeneView

GeneView via analysis of contig annotation: ANKH ankylosis, progressive homolog (mouse)

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_054027

function

HuRef

NW_001838927->NM_054027

function

Celera

NW_922518->NM_054027

function

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


reference	NT_006576->NM_054027->NP_473368	14777064	reverse	intron

HuRef	NW_001838927->NM_054027->NP_473368	7036206	reverse	intron

Celera	NW_922518->NM_054027->NP_473368	13913463	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs25946 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_001838927.1	7036206	14760108	plus	C	alt_assembly_8	HuRef	HuRef	view	740
5	NW_922518.1	13913463	14811031	plus	C	alt_assembly_1	Celera	Celera	view	740
5	NT_006576.15	14777064	14840064	plus	A	ref_assembly	reference	reference	view	740

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023089 AC016649 AC022496.15 AC025456 AC025456.3 AC026437 AC026437.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss10236136	HapMap-CEU	European	120	IG	0.250	0.583	0.167	0.200	0.542	0.458

	HapMap-HCB	Asian	90	IG	0.067	0.444	0.489	0.584	0.289	0.711

	HapMap-JPT	Asian	90	IG	0.022	0.222	0.756	1.000	0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	IG	0.333	0.517	0.150	0.655	0.592	0.408

ss66452213	HapMap-CEU	European	118	GF	0.254	0.593	0.153		0.551	0.449

	HapMap-HCB	Asian	90	GF	0.067	0.444	0.489		0.289	0.711

	HapMap-JPT	Asian	90	GF	0.022	0.222	0.756		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF	0.333	0.517	0.150		0.592	0.408

ss68928188	HapMap-CEU	European	120	GF	0.250	0.583	0.167		0.542	0.458

	HapMap-HCB	Asian	90	GF	0.067	0.444	0.489		0.289	0.711

	HapMap-JPT	Asian	90	GF	0.022	0.222	0.756		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF	0.333	0.517	0.150		0.592	0.408

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.486+/-0.084	270	210	270	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 .