Reference SNP(refSNP) Cluster Report: rs4253211

Reference SNP(refSNP) Cluster Report: rs4253211

refSNP ID: rs4253211
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
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_000124.1:c.3689G>C
NP_000115.1:p.R1230P
NT_017696.14:g.1482780C>G
NT_017696.14:g.1482781C>G
XM_001719050.1:c.28-1631C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76884572 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4253211 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
ss5609194	EGP_SNPS\|ERCC6-069728	fwd/B	C/G	ctcgaattccacacctggtgaagaaaaggc	ttaccagaagcaagacagtgaaaacaagag	01/08/03	04/07/04	111	Genomic	unknown
ss24205469	PERLEGEN\|afd2243442	rev/T	C/G	ctcttgttttcactgtcttgcttctggtaa	gccttttcttcaccaggtgtggaattcgag	08/10/04	09/13/04	123	Genomic	unknown
ss48294101	SNP500CANCER\|ERCC6-03	fwd/	C/G	ctcgaattccacacctggtgaagaaaaggc	ttaccagaagcaagacagtgaaaacaagag	08/19/05	11/03/06	126	Genomic	unknown
ss48430834	APPLERA_GI\|hCV25762749	fwd/	C/G	ctcgaattccacacctggtgaagaaaaggc	ttaccagaagcaagacagtgaaaacaagag	10/02/05	11/03/06	126	Genomic	unknown
ss65728211	ILLUMINA\|Human1-rs4253211	fwd/B	C/G	ctcgaattccacacctggtgaagaaaaggc	ttaccagaagcaagacagtgaaaacaagag	10/10/06	10/10/06	127	Genomic	unknown
ss66861974	EGP_SNPS\|ERCC6_069728	fwd/	C/G	ctcgaattccacacctggtgaagaaaaggc	ttaccagaagcaagacagtgaaaacaagag	11/09/06	12/16/06	127	Genomic	unknown
ss69078417	PERLEGEN\|PGP02243442	rev/	C/G	ctcttgttttcactgtcttgcttctggtaa	gccttttcttcaccaggtgtggaattcgag	01/30/07	03/31/08	127	Genomic	unknown
ss74809099	AFFY\|SNP_M-181657	fwd/B	C/G	ctcgaattccacacctggtgaagaaaaggc	ttaccagaagcaagacagtgaaaacaagag	08/09/07	08/09/07	128	Genomic	unknown
ss76463408	AFFY\|AFFY_6_1M_SNP_A-8324367	rev/	C/G	gtcttgcttctggtaa	gccttttcttcaccag	08/28/07	08/30/07	130	Genomic	unknown
ss76884572	SI_EXO\|NT_017696.14_1482781	rev/	C/G	ctcttgttttcactgtcttgcttctggtaa	gccttttcttcaccaggtgtggaattcgag	09/20/07	09/20/07	129	Genomic	unknown
ss86347107	CANCER-GENOME\|492	rev/	C/G	ctcttgttttcactgtcttgcttctggtaa	gccttttcttcaccaggtgtggaattcgag	01/25/08	01/25/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATGAGTAGTA ATGTAACTAG CAATGATAGG CTTGGAGAAG AGACAAATGC AGTATCTGGA
 CCAGAAGAGT TGTCAGTGAT TAGTGGAAAT GGGGAATGTT CAAATTCTTC AGGAACAGGC
 AAAACTTCTA TGCCATCTGG TGATGAAAGC ATTGATGAAA AGTTAGGTCT TTCTTACAAA
 AGAGAAAGAC CCAGCCAGGC TCAAACAGAA GCTTTTTGGG AGAATAAACA AATGGAAAAT
 AATTTTTATA AGCACAAGTC AAAAACAAAA CATCATAGTG TGGCAGAAGA AGAGACCCTG
 GAGAAACATC TGAGACCAAA GCAAAAGCCT AAGAACTCTA AGCATTGCAG AGACGCCAAG
 TTTGAAGGAA CTCGAATTCC ACACCTGGTG AAGAAAAGGC
 S
 TTACCAGAAG CAAGACAGTG AAAACAAGAG TGAGGCCAAG GAACAGAGCA ATGACGATTA
 TGTTTTGGAA AAGCTTTTCA AAAAATCAGG TAATCCATTT GATACGTTTG CCACAGGGAT
 GCTAGGATTA GAAAATGAGT AGGCTGTTTC TAGCAGTAGC AGTCTTTAAC TGATGGTGCA
 TAGAGGGCTG TCAGCCATTA GTGTTTTTCT TCAAAAATTT AGATTTGAAA TATATTGACA
 TTTTAAAAAT CGTATTTACA CCTCTTTTCT GAAGACCTAG AATAATTTGA AACTTTGGAA
 AACAATAGTA CTTATGGCCA CTCATGGGAG GTGTGCAATT CTTAAATCGA TGTGTACTAC
 CTGAACATTA GTAGGCAGTT ACTTTACATG CTATATGCTA

GeneView

GeneView via analysis of contig annotation: LOC100128032 hypothetical protein LOC100128032

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_017696->XM_001719050

function

HuRef

NW_001837975->XM_001719359

function

Celera

NW_924685->XM_001718989

function

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


reference	NT_017696->XM_001719050->XP_001719102	1482781	forward	intron

HuRef	NW_001837975->XM_001719359->XP_001719411	394431	reverse	intron

Celera	NW_924685->XM_001718989->XP_001719041	1306635	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4253211 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_924685.1	1306635	44264481	minus	C	alt_assembly_1	Celera	Celera	view	300
10	NW_001837975.2	394431	44943132	plus	G	alt_assembly_8	HuRef	HuRef	view	300
10	NT_017696.14	1482781	50348323	minus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_017696.14

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_000124.1	AL138760.14

UniGene Cluster ID
133444

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss24205469	AFD_EUR_PANEL	European	48	IG		0.083	0.917	1.000	0.042	0.958

	AFD_AFR_PANEL	African American	46	IG			1.000			1.000

	AFD_CHN_PANEL	Asian	48	IG		0.167	0.833	0.752	0.083	0.917

ss48294101	P1		200	AF		0.150	0.850	0.439	0.075	0.925

	CAUC1		60	AF		0.200	0.800	0.584	0.100	0.900

	AFR1		48	AF		0.083	0.917	1.000	0.042	0.958

	HISP1		44	AF		0.136	0.864	0.752	0.068	0.932

	PAC1		48	AF		0.167	0.833	0.655	0.083	0.917

ss48430834	HapMap-CEU	European	120	IG		0.217	0.783	0.371	0.108	0.892

	HapMap-HCB	Asian	90	IG		0.089	0.911	1.000	0.044	0.956

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

	HapMap-YRI	Sub-Saharan African	120	IG			1.000			1.000

	AGI_ASP population	multiple	78	IG		0.154	0.846	0.655	0.077	0.923

ss5609194	PDR90	Global	168	IG		0.167	0.833	0.439	0.083	0.917

ss66861974	HSP_GENO_PANEL		120	IG		0.133	0.867	0.584	0.067	0.933

	CEU_GENO_PANEL	European	120	IG		0.217	0.783	0.371	0.108	0.892

	AAM_GENO_PANEL	African American	124	IG		0.016	0.984	1.000	0.008	0.992

	CHB_GENO_PANEL	Asian	88	IG		0.068	0.932	1.000	0.034	0.966

	YRI_GENO_PANEL	Sub-Saharan African	120	IG			1.000			1.000

	JPT_GENO_PANEL	Asian	88	IG	0.023	0.250	0.727	1.000	0.148	0.852

ss69078417	HapMap-CEU	European	120	GF		0.217	0.783		0.108	0.892

	HapMap-HCB	Asian	90	GF		0.089	0.911		0.044	0.956

	HapMap-JPT	Asian	90	GF	0.022	0.244	0.733		0.144	0.856

	HapMap-YRI	Sub-Saharan African	120	GF			1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.126+/-0.217	584	512	270	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .