Reference SNP(refSNP) Cluster Report: rs25957

Reference SNP(refSNP) Cluster Report: rs25957

refSNP ID: rs25957
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_054027.3:c.97-13932G>C
NT_006576.15:g.14773232C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2395917 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs25957 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
ss30800	KWOK\|OVLP-12682	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	04/28/00	10/10/03	76	Genomic	99 %
ss32851	KWOK\|OVLP-23499	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	04/28/00	10/10/03	76	Genomic	99 %
ss32920	KWOK\|OVLP-23588	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	04/28/00	10/10/03	76	Genomic	99 %
ss633104	SC_JCM\|AC016649.3_75142	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	07/12/00	10/10/03	80	Genomic	unknown
ss1117934	KWOK\|OVLP-000804-295753	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	09/02/00	10/10/03	86	Genomic	99 %
ss1119698	KWOK\|OVLP-000804-306485	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	09/02/00	10/10/03	86	Genomic	99 %
ss1120013	KWOK\|OVLP-000804-308334	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	09/02/00	10/10/03	86	Genomic	99 %
ss1790729	KWOK\|OVLP-000925-516846	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	10/05/00	10/10/03	89	Genomic	99 %
ss1791406	KWOK\|OVLP-000925-524116	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	10/05/00	10/10/03	89	Genomic	99 %
ss1791948	KWOK\|OVLP-000925-530262	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	10/05/00	10/10/03	94	Genomic	99 %
ss2395917	TSC-CSHL\|TSC0437390	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	10/20/00	08/05/04	88	Genomic	95 %
ss5168419	TSC-CSHL\|TSC0437931	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	09/19/02	10/10/03	108	Genomic	unknown
ss10191357	BCM_SSAHASNP\|chr5.NT_023089.13_14765970	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	06/27/03	10/10/03	116	Genomic	unknown
ss14846823	SC_SNP\|NT_023089.13_14765970	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	11/12/03	11/22/03	119	Genomic	unknown
ss22221947	SSAHASNP\|WGSA-200403-chr5.chr5.NT_023089.13_14765970	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	03/21/04	03/21/04	121	Genomic	unknown
ss24357063	PERLEGEN\|afd4047629	fwd/T	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	08/10/04	09/13/04	123	Genomic	unknown
ss82824981	HGSV\|Cor18555_SNV_20070510.chr5_14836232	fwd/	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	11/27/07	12/03/07	130	Genomic	unknown
ss93002108	BCMHGSC_JDW\|JWB-1939776	fwd/	C/G	tgagttctaagggtctggggcacttgatct	gttgtttttaggaggtgagagagagttaaa	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 GTTAGAACTC ACTATTGGTA TTTATGTAAC TGGCACGCAT CAAGTTTTGT GAATGAGTTC
 TAAGGGTCTG GGGCACTTGA TCT
 S
 GTTGTTTTTA GGAGGTGAGA GAGAGTTAAA AGCAGTCATT AAACAAGTTA GTCTGCTCAG
 CCCATGACCA GTCTCACTGA GCCATTTGTT AGGAATCAGT AACACTGCCT ATAACTATCA
 GGACAAGAGA AGACACTGTG GCACAGAAGA GGGTCGCCAC CATTCTacac acacacacac
 acacacacac acacacacac acacacacca cacaTGGAGA TAGGAATCTC AGCAAAATTA
 AAATAGCACT ATTTTACTTA ATTGTGACAA GGCTGTCTTC AGCATTTGCT TTGCTGTGTG
 CAAGTAGGAA TGTCATTACC TTGCCATCCC ATGCTACTGT TATTGGTTTA AATTATTGAT
 GCACAGTATT CTATTGATGC ACAGTATTCT AGTTGAAGTA AAATTGTCTC AAGGAATTAA
 GCTGTTTAGA ACACAATACA AGAAAGGACA AAGGATATGA TCATGGCACC CCAAAAATTT
 GCAGAGTCAA CAGTGTCACT GGTTGTAACA GCAATTTAAG AATTATATGT CCTGAATTTA
 TTTTGTCTTT ACAATGATAT CCATGGTTTA TACCTAAGGT TTTTCACCTT AAATAGTGAC
 ATGATAATGT AATAAGCTAG AGAATAACGT GAATAAAATT AAAGTGCTTT GAAAATTGCT
 AA

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	14773232	reverse	intron

HuRef	NW_001838927->NM_054027->NP_473368	7032381	reverse	intron

Celera	NW_922518->NM_054027->NP_473368	13909632	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs25957 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	7032381	14756283	plus	G	alt_assembly_8	HuRef	HuRef	view	83
5	NW_922518.1	13909632	14807200	plus	C	alt_assembly_1	Celera	Celera	view	83
5	NT_006576.15	14773232	14836232	plus	C	ref_assembly	reference	reference	view	83

NCBI Resource Links

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

dbSNP Blast Analysis
GenBank HTGS Finished:
AC025456.7 AC026437.5 NC_000005.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss2395917	HapMap-CEU	European	120	IG	0.017	0.450	0.533	0.100	0.242	0.758

	HapMap-HCB	Asian	86	IG		0.372	0.628	0.150	0.186	0.814

	HapMap-JPT	Asian	88	IG		0.136	0.864	0.655	0.068	0.932

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.350	0.617	0.655	0.208	0.792

ss24357063	AFD_EUR_PANEL	European	46	IG	0.087	0.391	0.522	1.000	0.283	0.717

	AFD_AFR_PANEL	African American	42	IG	0.095	0.238	0.667	0.200	0.214	0.786

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.292	0.667	1.000	0.188	0.812

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.313+/-0.242	332	260	9	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 .