Reference SNP(refSNP) Cluster Report: rs1018171

Reference SNP(refSNP) Cluster Report: rs1018171

refSNP ID: rs1018171
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_030790.3:c.1453+14699G>A
NT_010498.15:g.852279C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14267244 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1018171 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss1482154	TSC-CSHL\|TSC0221508	fwd/T	A/G	ccatggaaagattttactggggataaaaat	ctaataatatatgtattggacaaaattaca	09/07/00	04/07/04	86	Genomic	95 %
ss14267244	BCM_SSAHASNP\|chr16.NT_035363.3_852279	rev/B	C/T	tgtaattttgtccaatacatatattattag	atttttatccccagtaaaatctttccatgg	11/05/03	10/25/06	119	Genomic	unknown
ss23508506	PERLEGEN\|afd4654980	rev/B	C/T	tgtaattttgtccaatacatatattattag	atttttatccccagtaaaatctttccatgg	08/10/04	09/13/04	123	Genomic	unknown
ss43921600	ABI\|hCV8919276	rev/B	C/T	tgtaattttgtccaatacatatattattag	atttttatccccagtaaaatctttccatgg	07/18/05	11/03/06	126	Genomic	unknown
ss75090959	ILLUMINA\|ILMN_Human_1M_rs1018171	fwd/T	A/G	ccatggaaagattttactggggataaaaat	ctaataatatatgtattggacaaaattaca	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GTTGGAGTCA CTGAGGGAAG GAATGACTCA CAGAAATTCA AACTTTGAAA TCATAAAGTA
 GTTGTTTTGA AATTTTTGTT ATGGAAGCTT GTTACCAAGG GTGAATCTTC GGCAGGGTTG
 GTATAGGTGT GGTTGACAAA ATTTAGCTAT AACAAGTGGG CTGTCAGATG CCATGGAAAG
 ATTTTACTGG GGATAAAAAT
 R
 CTAATAATAT ATGTATTGGA CAAAATTACA TTTTTATATG GGACCATGGA CAGTTTTTCT
 TAGCATCACC ACCATATTTG GCAGGGGTGG GGACTTTTCA TTTTTGtttt aaattgtggt
 gaaatacata taaacataaa atatatcatc ttaaccattt ttaagtatac agttcagtag
 tactaagtgt attcacactg tgtgcaacca tcaccatcat tactctccag agcacttcac
 cttgcagact tgaaactctg tacccattaa acgctaactc cccatttccc tcctgctcca
 gcccatggca tgtaccattc taccttcagt ctctatgaat ctgagtactc taggtcaggg
 gtgcccatcc cccaggccac agaccagtac caatccatgg cctgttagga accgggccac
 atagcaggag gtgagcagca ggtgagcaag caaagcttca tctgtattta cagctgctcc
 ccatcaatca cattatagcc

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	852279	reverse	intron

HuRef	NW_001838287->NM_030790->NP_110417	650470	forward	intron

Celera	NW_926462->NM_030790->NP_110417	810847	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1018171 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	810847	31746048	minus	C	alt_assembly_1	Celera	Celera	view	200
16	NW_001838287.2	650470	33128712	plus	G	alt_assembly_8	HuRef	HuRef	view	200
16	NT_010498.15	852279	45795581	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_035363 AC027470.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC007494.8 NC_000016.8	AC027467.4 AC027470.2 CT009498.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss14267244	HapMap-CEU	European	120	IG		0.083	0.917	0.752	0.042	0.958

	HapMap-HCB	Asian	90	IG		0.044	0.956	1.000	0.022	0.978

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.533	0.383	0.200	0.350	0.650

ss1482154	TSC_42_AA		82	AF					0.270	0.730

	TSC_42_C		84	AF					0.050	0.950

	TSC_42_A		78	AF					0.010	0.990

ss23508506	AFD_EUR_PANEL	European	48	IG		0.083	0.917	1.000	0.042	0.958

	AFD_AFR_PANEL	African American	46	IG	0.130	0.435	0.435	1.000	0.348	0.652

	AFD_CHN_PANEL	Asian	48	IG		0.083	0.917	1.000	0.042	0.958

ss43921600	AoD_African_American		90	AF					0.290	0.710

	AoD_Caucasian		92	AF					0.040	0.960

	AoD_Chinese		90	AF					0.030	0.970

	AoD_Japanese		90	AF					0.010	0.990

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.216+/-0.248	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .