Reference SNP(refSNP) Cluster Report: rs11869820

Reference SNP(refSNP) Cluster Report: rs11869820

refSNP ID: rs11869820
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:	G/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_019020.2:c.1908+515A>C
NT_024871.11:g.321731T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss17584292 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11869820 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
ss17584292	CSHL-HAPMAP\|CSHL-HuCC-200402.chr17.NT_024871.11_321731		fwd/B	G/T	acagagccagtgctgtgctccaaggggaat	tgctgagaagatgctggtgacggtggacgg	02/19/04	10/26/06	120	Genomic			unknown

Fasta sequence (Legend)

 GGAGGCTGCT GGAGCTGCCG TGGTGGATAG AGCCAGCTCC TGCAAAAGGG TCCAGCCCTC
 CTGGATGCGT CGATGTGAGT TTTTTTTTTA AAAGGCTGAT GGACTCAAAG AGACTTGCTT
 ATCTTTTGAC ATCTCCAGCT TGTCCCTAGT TTGGGCGTTA AGGCCATGTG ACAGAGCCAG
 TGCTGTGCTC CAAGGGGAAT
 K
 TGCTGAGAAG ATGCTGGTGA CGGTGGACGG AGAGTGGAAG TCGGTATCAC TGATTGGGGC
 CCTCTGGAGG GGCCGACAGG GAAGTGGGAT CTCAGGCCCT TTCTCTGCAC AGCAGGGTAA
 CGGGTGAGTC GGCCCTCGTG GCAGGGCGGT CCCGAGGGGG TGGAGCGGTG CTGGCTCACG
 CTCGTGGGCA CCAGCGTCCT

GeneView

GeneView via analysis of contig annotation: TBC1D16 TBC1 domain family, member 16

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_024871->NM_019020

function

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


reference	NT_024871->NM_019020->NP_061893	321731	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11869820 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838456.2	79230	73358789	minus	A	alt_assembly_8	HuRef	HuRef	view	200
17	NW_926918.1	15049716	74544315	plus	T	alt_assembly_1	Celera	Celera	view	200
17	NT_024871.11	321731	75532787	plus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024871

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/T	T/T	HWP	G	T
ss17584292	HapMap-CEU	European	118	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG	0.022	0.978	1.000	0.011	0.989

	HapMap-JPT	Asian	90	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	114	IG	0.070	0.930	1.000	0.035	0.965

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.024+/-0.107	270	210	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 .