Reference SNP(refSNP) Cluster Report: rs2671894

Reference SNP(refSNP) Cluster Report: rs2671894

refSNP ID: rs2671894
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NM_020731.3:c.492C>T
NP_065782.2:p.H164H
NT_006576.15:g.412881C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss6903634 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2671894 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss3770624	SC_JCM\|AC060789.2_142061		fwd/T	A/G	ctgccggcagaagtcctggcggtcgtccac	tggatgtagtcataaatgttctggtgcatt	09/25/01	10/10/03	100	Genomic			unknown
ss6903634	SNP500CANCER\|AHRR-04		rev/B	C/T	aatgcaccagaacatttatgaytacatcca	gtggacgaccgccaggacttctgccggcag	02/14/03	04/07/04	113	Genomic			unknown

Fasta sequence (Legend)

 GGAGGGACAT GGGAGGAGGC CTCTGAAGAA AGGTGAGATT TGGCGCTAAG GTCAATGTGT
 AAGGCAAAGC ACACCAAGAA GGTGCGACAG GGTCATTTCC AGAGGCAGCG AYGTGTTATG
 GGACCTGCTT TAGGTTTTGC TGACTCACTT GGACCCCAGA CACCCACCTG TCTCCAAGGG
 CGGGGSCTGC CCAAACACCA CCTGGGGAGG GTCCATGGCC CAGTGGAGCT GCCGGCAGAA
 GTCCTGGCGG TCGTCCAC
 R
 TGGATGTART CATAAATGTT CTGGTGCATT ACATCCGTCT GAAATAGCGC AACAAGATTA
 TTTCAGCCTT ACCCCAAGTG GCTTTAGACA CTTTATTCCA CCGACGAGTA ACCGAAAAAT
 TTCCACTCCA CTTGTCAAAG CAAGTCACAG CCACAGGGAG AGAATCCCAC CGAAGAGACG
 GCG

GeneView

GeneView via analysis of contig annotation: AHRR aryl-hydrocarbon receptor repressor

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_020731

function

HuRef

NW_001838923->NM_020731

function

Celera

NW_922496->NM_020731

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_006576->NM_020731->NP_065782	412882	forward	536	synonymous	T	His [H]	3	164
					contig reference	C	His [H]	3	164

HuRef	NW_001838923->NM_020731->NP_065782	1712074	reverse	536	synonymous	T	His [H]	3	164
					contig reference	C	His [H]	3	164

Celera	NW_922496->NM_020731->NP_065782	408886	forward	536	synonymous	T	His [H]	3	164
					contig reference	C	His [H]	3	164

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2671894 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_001838923.2	1712074	410897	plus	G	alt_assembly_8	HuRef	HuRef	view	258
5	NT_006576.15	412882	475882	minus	C	ref_assembly	reference	reference	view	258
5	NW_922496.1	408886	520958	minus	C	alt_assembly_1	Celera	Celera	view	258

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034766.2 AC010442 AC061972 AC061974 AC084098

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC010442.7 NC_000005.8	AC060789.2 AC061974.2 AC084098.5 AC113363.1 AC138431.1

UniGene Cluster ID
50823

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss6903634	P1		202	GF	0.010	0.990	1.000	0.005	0.995

	CAUC1		60	GF		1.000			1.000

	AFR1		48	GF	0.042	0.958	1.000	0.021	0.979

	HISP1		46	GF		1.000			1.000

	PAC1		48	GF		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.010+/-0.070	0	0	0	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 .