Reference SNP(refSNP) Cluster Report: rs4647189

Reference SNP(refSNP) Cluster Report: rs4647189

refSNP ID: rs4647189
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
Map to Genome Build:	36.3

Allele
Variation Class:	DIP: deletion/insertion polymorphism
RefSNP Alleles:	-/AAAC
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NT_007592.14:g.22396677_22396680del4

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss6312866 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4647189 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
ss6312866	EGP_SNPS\|LTA-000261		fwd/B	-/AAAC	cattttttgtgttagacaaaaactagaaac	caaatccccatcaacagaatatattagaat	01/21/03	04/07/04	111	Genomic			unknown

Fasta sequence (Legend)

 ACAGTGGGCT TTACCCCGGG TCACCACCAG CCCCAGCTCC AACCCCTCTA ACACTCTCCA
 AGTAAAATCA CATCAGTAGC AGTAATAATA TTTGAGGTGA CAAGTTGGTA TTATCTCAAA
 CTTAGGAAAA GTGAATAAAG TCATCTTTAG AAACTGCTTT TTTTAAACCT TGTAACTTGC
 AAGCTAAGTG AAAATGGGCT catgtatgag aatgttcgtg ttagacattt tttgtgttag
 acaaaaacta gaaac
 N
 caaatcccca tcaacagaat atattagaat atattgatac aatagaatat tacatcataa
 ttttttttaa aaacattact gatacataca accacgtata tgaatctcac aaacataatg
 ctgactgaaa gaagtcaaac agaaatgagt acattctgtg tgatttcatt tatatgatgc
 cccaaaccag gaggaaataa tctatggtga taaaagtgag agagtggttg gttatctttg
 gagggtaTCA GCAGG

GeneView

GeneView via analysis of contig annotation: LTA lymphotoxin alpha (TNF superfamily, member 1)

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_007592->NM_000595

function

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


reference	NT_007592->NM_000595->NP_000586	22396677:22396680	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4647189 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838980.1	4597467..4597470	31325158..31325161	plus	AAAC	alt_assembly_8	HuRef	HuRef	view	255
6	NT_007592.14	22396677..22396680	31646405..31646408	plus	AAAC	ref_assembly	reference	reference	view	255
6	NT_113894.1	99999..100002	31671519..31671522	plus	AAAC	alt_assembly_4	c6_QBL	c6_QBL	view	255
6	NT_113891.1	2984550..2984553	31673093..31673096	plus	AAAC	alt_assembly_3	c6_COX	c6_COX	view	255
6	NW_923073.1	4600962..4600965	33136641..33136644	plus	AAAC	alt_assembly_1	Celera	Celera	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY216498

dbSNP Blast Analysis
GenBank HTGS Finished:
AL662801.7 AL662847.6 AL929587.5 BX248519.7 BX927320.5 CR753892.5 CR942185.8

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	-/AAAC	AAAC/AAAC	HWP	-	AAAC
ss6312866	PDR90	Global	120	IG	0.033	0.967	1.000	0.017	0.983

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.033+/-0.124	90	90	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 .