Reference SNP(refSNP) Cluster Report: rs35737009

Reference SNP(refSNP) Cluster Report: rs35737009

refSNP ID: rs35737009
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	126/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_003327.2:c.145+47G>C
NT_004350.18:g.627948C>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss46533263 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs35737009 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
ss46533263	EGP_SNPS\|TNFRSF4-002192		fwd/	C/G	ggtcgccacgcacgggcactccagggactg	gggctggggcagggatgggccagccaggag	07/25/05	11/03/06	126	Genomic			unknown

Fasta sequence (Legend)

 TCCACAGTCC TTATAGCCAC ACCCCGCAAG GAAAACCCAG ACTCTGGCGA CAGCAGAGAC
 GAGGATGTGC GTGGGGGCTC GGCGGCTGGG CCGCGGGCCG TGTGCGGCTC TGCTCCTCCT
 GGGCCTGGGG CTGAGCACCG TGACGGGGCT CCACTGTGTC GGGGACACCT ACCCCAGCAA
 CGACCGGTGC TGCCACGAGT GCAGGCCAGG TGAGGCCTCA GGAGGGGTCG CCACGCACGG
 GCACTCCAGG GACTG
 S
 GGGCTGGGGC AGGGATGGGC CAGCCAGGAG GCTGGTCCTG GGGAGGGGGC GGGTGAGGGG
 CCGGCCAAGC CTGGCAGAGG AGCCGCCTGG GGGGGTCCAC GGGCGCAAGC CTGGGGCCTG
 ACCGCTGCCT GACGCCGGCC TCTGCTGCAG GCAACGGGAT GGTGAGCCGC TGCAGCCGCT
 CCCAGAACAC GGTGTGCCGT CCGTGCGGGC CGGGCTTCTA CAACGACGTG GTCAGCTCCA
 AGCCGTGCAA GCCCT

GeneView

GeneView via analysis of contig annotation: TNFRSF4 tumor necrosis factor receptor superfamily, member 4

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_004350->NM_003327

function

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


reference	NT_004350->NM_003327->NP_003318	627948	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs35737009 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838585.1	401767	421014	minus	C	alt_assembly_8	HuRef	HuRef	view	255
1	NT_004350.18	627948	1139179	minus	C	ref_assembly	reference	reference	view	255
1	NW_921350.1	1434338	1434338	plus	G	alt_assembly_1	Celera	Celera	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
DQ118974

dbSNP Blast Analysis
GenBank HTGS Finished:
AL162741.44

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss46533263	EGP_YORUB-PANEL	Sub-Saharan African	24	AF	0.083	0.250	0.667	0.403	0.208	0.792

	EGP_HISP-PANEL	Hispanic	42	AF		0.048	0.952	1.000	0.024	0.976

	EGP_CEPH-PANEL	European	44	AF			1.000			1.000

	EGP_AD-PANEL	African American	30	AF	0.067	0.200	0.733	0.294	0.167	0.833

	EGP_ASIAN-PANEL	Asian	48	AF	0.042	0.167	0.792	0.251	0.125	0.875

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.164+/-0.235	95	95	0	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 .