Reference SNP(refSNP) Cluster Report: rs16953990

Reference SNP(refSNP) Cluster Report: rs16953990

refSNP ID: rs16953990
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
Map to Genome Build:	36.3

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

HGVS Names
NM_030790.3:c.1374+2670C>A
NT_010498.15:g.883405G>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss23508747 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16953990 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
ss23508747	PERLEGEN\|afd3707345		fwd/B	G/T	aggtactggcagaagtaatgttggtgtgtg	taactaaataaggaggtgggcaaagacaat	08/10/04	09/13/04	123	Genomic			unknown

Fasta sequence (Legend)

 GCTGGACTAA CCCAGGGTTG AAATTTTCCC AGGCAGGTAC ACTGGAAAGT CAGTGCTTTA
 TAGGAGTTAA AGGTACTGGC AGAAGTAA
 TGTTGGTGTG TG
 K
 TAACTAAATA AG
 GAGGTGGGCA AAGACAATAC TGGGCTGATA CAGGTCAAGA GACTAATGGT TTTAAAGTGG
 AACAGGTATA ATTAGAGTAA CAGAGTGG

GeneView

GeneView via analysis of contig annotation: ITFG1 integrin alpha FG-GAP repeat containing 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_010498->NM_030790

function

HuRef

NW_001838287->NM_030790

function

Celera

NW_926462->NM_030790

function

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


reference	NT_010498->NM_030790->NP_110417	883405	reverse	intron

HuRef	NW_001838287->NM_030790->NP_110417	619350	forward	intron

Celera	NW_926462->NM_030790->NP_110417	841966	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs16953990 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_926462.1	841966	31777167	plus	G	alt_assembly_1	Celera	Celera	view	100
16	NW_001838287.2	619350	33159832	minus	C	alt_assembly_8	HuRef	HuRef	view	100
16	NT_010498.15	883405	45826707	plus	G	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000016.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC007494.8 NC_000016.8	AC027467.4 AC027470.2

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	HWP	G	T
ss23508747	AFD_EUR_PANEL	European	48	IG	1.000			1.000

	AFD_AFR_PANEL	African American	46	IG	0.913	0.087	1.000	0.957	0.043

	AFD_CHN_PANEL	Asian	48	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.028+/-0.115	71	50	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 .