Reference SNP(refSNP) Cluster Report: rs11567704

Reference SNP(refSNP) Cluster Report: rs11567704

refSNP ID: rs11567704
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002185.2:c.132C>T
NP_002176.2:p.S44S
NT_006576.15:g.35833759C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48428323 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11567704 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
ss16336639	PGA-UW-FHCRC\|IL7R-005968		fwd/B	C/T	actggatgactactcattctcatgctatag	cagttggaagtgaatggatcgcagcactca	12/01/03	02/03/05	120	Genomic			unknown
ss48428323	APPLERA_GI\|hCV25616826		fwd/B	C/T	actggatgactactcattctcatgctatag	cagttggaagtgaatggatcgcagcactca	09/28/05	11/03/06	126	Genomic			unknown

Fasta sequence (Legend)

 ATGATGGATT TTTTTTTTCT ATTGGAAAAC TCTGTTAGCA TTGAGCGTTT TTGTTTTTTG
 TTTTTTGTTG GTTGGTTGGT TTTGAAGCAT TTTTCTTGTC TTTGCCCTTG GGCTTTTCTT
 CCTTGAATAC TACATAATCC ATTACTATTT CATGTCTGCC ACAGAGTCTG CTATTTTATT
 AAGGTCATGC CATATTTCAA AAGGATGCAT TTATTTGTTT CATTAACAGC TGCATGTTTG
 TTCCTCCCCA GGAGACTTGG AAGATGCAGA ACTGGATGAC TACTCATTCT CATGCTATAG
 Y
 CAGTTGGAAG TGAATGGATC GCAGCACTCA CTGACCTGTG CTTTTGAGGA CCCAGATGTC
 AACACCACCA ATCTGGAATT TGAAATATGG TGAGGGATGG TGGTTTTAAT GGTTGCTTAG
 ACATCCTCTG TCTCTCTTTT CATATGCTCT TTTTAGTAGC CACAAAAGAA AGAATATGTG
 GCCTAATTAA CAAATGTTAA CATCTAAGGA ATTCCCAAAG GCCTCCTGAA ACTCCTTGTC
 CTTCACCAAA AACACTCATA CAAAGCTCCT CTCACGGTTC AGCTTTCAGA CCCTGAGACT

GeneView

GeneView via analysis of contig annotation: IL7R interleukin 7 receptor

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_002185

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_002185->NP_002176	35833760	forward	221	synonymous	T	Ser [S]	3	44
					contig reference	C	Ser [S]	3	44

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11567704 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_922596.1	1457218	35746704	plus	C	alt_assembly_1	Celera	Celera	view	300
5	NW_001838933.1	153641	35811030	plus	C	alt_assembly_8	HuRef	HuRef	view	300
5	NT_006576.15	35833760	35896760	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
AY449709

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_002185.2 XM_001127146.1

UniGene Cluster ID
362807

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss16336639	PGA-AFRICAN-PANEL	African American	48	IG	0.958	0.042	1.000	0.979	0.021

	PGA-EUROPEAN-PANEL	European	46	IG	1.000			1.000

ss48428323	HapMap-CEU	European	118	IG	1.000			1.000

	HapMap-HCB	Asian	90	IG	1.000			1.000

	HapMap-JPT	Asian	90	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	0.983	0.017	1.000	0.992	0.008

	AGI_ASP population	multiple	76	IG	0.974	0.026	1.000	0.987	0.013

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.010+/-0.071	346	274	9	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 .