Reference SNP(refSNP) Cluster Report: rs11076654

Reference SNP(refSNP) Cluster Report: rs11076654

refSNP ID: rs11076654
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:	A/T
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001042610.1:c.319+1107A>T
NM_024043.2:c.379+1107A>T
NT_010542.15:g.1634702T>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43848489 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11076654 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
ss16712218	CSHL-HAPMAP\|CSHL-HuAA-200402.chr16.NT_010542.14_1629939	fwd/B	A/T	tgaccacccccacctttcgttcttggccca	tttatgatgaaaattcacattcattaaatt	02/17/04	03/04/04	120	Genomic	unknown
ss20022432	CSHL-HAPMAP\|CSHL-HuFF-200402.chr16.NT_010542.14_1629939	fwd/B	A/T	tgaccacccccacctttcgttcttggccca	tttatgatgaaaattcacattcattaaatt	02/21/04	03/04/04	120	Genomic	unknown
ss43848489	ABI\|hCV2875837	fwd/	A/T	tgatcacccccacctttcgttcttggccca	tttatgatgaaaattcacattcattaaatt	07/18/05	03/31/08	126	Genomic	unknown
ss66196332	AFFY\|SNP_A-2269389	rev/T	A/T	gaattttcatcataaa	tgggccaagaacgaaa	10/27/06	03/31/08	127	Genomic	unknown
ss76278747	AFFY\|AFFY_6_1M_SNP_A-2269389	rev/	A/T	gaattttcatcataaa	tgggccaagaacgaaa	08/28/07	08/30/07	129	Genomic	unknown
ss90501162	BCMHGSC_JDW\|JWB-0988862	fwd/	A/T	tgaccacccccacctttcgttcttggccca	tttatgatgaaaattcacattcattaaatt	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 AGAAGGCTCG GCCCTGATGC TCTCACAGTT ACTGAAGTTC ACACAGGTCA CGTCAGTGTC
 CTTCACTGGT CACTGTCAGA GACTGAGGAC GCGCTGTCGC ATCCTCATGA GTCCTGTGCT
 CTCGTCACGG CTTAGGAAGG AGACACGACA ATGGCCGTGC TGGGGGCCCT GCTCGGCAGT
 GTGAGGACAC TGGAGCTGCC TTCAGGCCAA TGGCAACGCT CCCGTGGGAA TCAGAGGAAG
 TTAAGTGAGC TGAGGAGGGG CCCGGGCTGG TGATCACCCC CACCTTTCGT TCTTGGCCCA
 W
 TTTATGATGA AAATTCACAT TCATTAAATT CTGCTTTTGA GGGGACAGTG GCTTTAGCCG
 TCTGTTGCTC ACTTGAAAAG TAAAGTTTTA AGCAGCTGTG ACGGGGAAGT TGCTTCAAGT
 TGGGCAGATA GCAGCGTGGT GAAATGAAGT GCTGAGGGAT TCTTGCTAAA ACACACGCAC
 ACCTCCCAGG ACTTCCCAAG GGGCCTCAGC CCACCACCCA CACCTCCCAG GACGTCCCAA
 GGGGCCTCAC CCCCCAAACA CACCTCCCAG GACTTCCCAA GGGGCCTCAC CCCCCAAACA

GeneView

GeneView via analysis of contig annotation: DBNDD1 dysbindin (dystrobrevin binding protein 1) domain 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_010542->NM_001042610

function

reference

NT_010542->NM_024043

function

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


reference	NT_010542->NM_001042610->NP_001036075	1634702	reverse	intron

reference	NT_010542->NM_024043->NP_076948	1634702	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11076654 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_926561.1	1706892	75138902	plus	T	alt_assembly_1	Celera	Celera	view	300
16	NW_001838336.2	100239	75766343	minus	A	alt_assembly_8	HuRef	HuRef	view	300
16	NT_010542.15	1634702	88601586	plus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010542

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/T	T/T	HWP	A	T
ss43848489	HapMap-CEU	European	120	IG	0.083	0.917		0.042	0.958

	HapMap-HCB	Asian	90	IG	0.178	0.822		0.089	0.911

	HapMap-JPT	Asian	88	IG	0.159	0.841		0.080	0.920

	HapMap-YRI	Sub-Saharan African	120	IG		1.000			1.000

ss66196332	HapMap-CEU	European	118	GF	0.068	0.932		0.034	0.966

	HapMap-HCB	Asian	90	GF	0.178	0.822		0.089	0.911

	HapMap-JPT	Asian	90	GF	0.089	0.911		0.044	0.956

	HapMap-YRI	Sub-Saharan African	120	GF		1.000			1.000

Concordant Genotype	Total Sample	A/T	T/T
ss43848489	267	19	247
ss66196332	266	18

RefSNP Genotype Summary	Total Individual	A/T	T/T
rs11076654	270	19	247

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5196	ss43848489	A/T	CSHL-HAPMAP	HapMap-JPT	NA18943	JA18943	r23_ch16_JPT_affymetrix:genechip500k
5196	ss66196332	A/A	CSHL-HAPMAP	HapMap-JPT	NA18943	JA18943	chr16-HapMap-JPT
5197	ss43848489	A/T	CSHL-HAPMAP	HapMap-JPT	NA18947	JA18947	r23_ch16_JPT_affymetrix:genechip500k
5197	ss66196332	A/A	CSHL-HAPMAP	HapMap-JPT	NA18947	JA18947	chr16-HapMap-JPT
5223	ss43848489	A/T	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	r23_ch16_JPT_affymetrix:genechip500k
5223	ss66196332	A/A	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	chr16-HapMap-JPT

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .