Reference SNP(refSNP) Cluster Report: rs181403

Reference SNP(refSNP) Cluster Report: rs181403

refSNP ID: rs181403
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_001196.2:c.12+218T>A
NM_197966.1:c.150+218T>A
NM_197967.1:c.-276-5874T>A
NT_011519.10:g.1384803A>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2065997 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs181403 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
ss240889	KWOK\|OVLP-000621-377291	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	06/30/00	10/10/03	79	Genomic	94 %
ss485856	SC_JCM\|AC007845.12_21604	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	07/12/00	10/10/03	87	Genomic	unknown
ss685017	SC_JCM\|AC007845.1_21604	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	07/27/00	10/10/03	87	Genomic	unknown
ss1053221	KWOK\|OVLP-000804-96217	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	09/02/00	10/10/03	86	Genomic	94 %
ss2065997	KWOK\|OVLP-000925-263719	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	10/07/00	10/10/03	87	Genomic	94 %
ss2066122	KWOK\|OVLP-000925-270416	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	10/07/00	10/10/03	87	Genomic	94 %
ss3365391	TSC-CSHL\|TSC1625077	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	09/20/01	10/10/03	100	Genomic	unknown
ss3554441	SC_JCM\|AC006285.11_137800	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	09/24/01	10/10/03	100	Genomic	unknown
ss7992710	SC_SNP\|NT_011519.9_1380634	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	04/15/03	10/10/03	114	Genomic	unknown
ss12583845	EGP_SNPS\|BID-026513	rev/B	A/T	tccctgtcctgcgccttcctcgcactccgc	tgtggtgcagcccctccacaccgcgcctgg	07/23/03	04/07/04	117	Genomic	unknown
ss24555157	PERLEGEN\|afd4311210	fwd/T	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	08/10/04	09/13/04	123	Genomic	unknown
ss44321293	ABI\|hCV2302712	fwd/	A/T	ccaggcgcggtgtggaggggctgcaccaca	gcggagtgcgaggaaggcgcaggacaggga	07/18/05	07/18/05	126	Genomic	unknown

Fasta sequence (Legend)

 TCTCCCCAGA CCATTTAAAG GGAAGGAGAG ACAAGGAAGC ATCCAGGGAG CGTCCTGCTG
 AAGGCGGGGG CTCCGGGCTC CCCTCCCAGA ACTCCACCGC ttttatcttt ataaagacgg
 ggtcttacta tgttgcccag gtttgtctca atcaaactcc tggcttcaag caatcctctc
 gcttctgcct cccaagtcac tgggattatg tgcctaagcc acctcgccca gcTATGAAGG
 GAAATTTAAA TCCAGTGGGT TAAAAAATTT TTGAAACACC TTACAGTTTA CAGTACTTTT
 ATTTGACCTT TATTGATTTA TTTGCTCCTC ATAGCAATGG CATTGGTTAG ACAAGGTAAG
 TATTGTCTTG CTTTTACAGT TGAGAGAATT ATATGAAGTG CTTATCTAAT GCCCCCTTTC
 TTCTTCTTAA ATCTCTTTCG TGTTTGTTTG GACAGggctg cagtgcagtg gcacaatcac
 agctcactgt agcctcgacc tcctggcctc aaggaatcct cctgccttgg cctcccaaag
 tgctgggacc cacagCCTAT GGCTGTTAAA TGGTCTTAAA CCCAAAGCCC CCTCGCCCTT
 GCAGTTAGCC CCAGGCGCGG TGTGGAGGGG CTGCACCACA
 W
 GCGGAGTGCG AGGAAGGCGC AGGACAGGGA AAGGTAGGAC TTCCCGGCTC CCGCCTGCTT
 CAGTGAAGGC GCTGGGCGGG GTTCGTCTGT GCCGAGCTGT GGTAAGGGCC AGGCGGGCTC
 AGCCTCAGCC CTCAGGGATG CGTGGTGGGG GACACGCAGG CCCTTACCCC TCGACCCCGC
 CCCCCACAAG GCACCCGCAG

GeneView

GeneView via analysis of contig annotation: BID BH3 interacting domain death agonist

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_011519->NM_001196

function

reference

NT_011519->NM_197966

function

reference

NT_011519->NM_197967

function

HuRef

NW_001838735->NM_197966

function

Celera

NW_927406->NM_001196

function

Celera

NW_927406->NM_197966

function

Celera

NW_927406->NM_197967

function

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


reference	NT_011519->NM_001196->NP_001187	1384803	reverse	intron

reference	NT_011519->NM_197966->NP_932070	1384803	reverse	intron

reference	NT_011519->NM_197967->NP_932071	1384803	reverse	intron

HuRef	NW_001838735->NM_197966->NP_932070	433451	forward	intron

Celera	NW_927406->NM_001196->NP_001187	1185352	reverse	intron

Celera	NW_927406->NM_197966->NP_932070	1185352	reverse	intron

Celera	NW_927406->NM_197967->NP_932071	1185352	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs181403 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_927406.1	1185352	1852352	plus	A	alt_assembly_1	Celera	Celera	view	640
22	NW_001838735.2	433451	2046883	minus	T	alt_assembly_8	HuRef	HuRef	view	640
22	NT_011519.10	1384803	16612653	plus	A	ref_assembly	reference	reference	view	640

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011519 AC006285 AC007845 AC007845.12 AC016025 AC016025.12

dbSNP Blast Analysis
GenBank HTGS Finished:
AC006285.13 AC007845.14 AC016025.14 NC_000022.9

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss12583845	PDR90	Global	164	IG	0.171	0.463	0.366	0.752	0.402	0.598

ss24555157	AFD_EUR_PANEL	European	48	IG	0.292	0.458	0.250	0.752	0.521	0.479

	AFD_AFR_PANEL	African American	44	IG	0.273	0.727		0.010	0.636	0.364

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.417	0.500	1.000	0.292	0.708

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.492+/-0.062	161	140	0	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

YES

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Revised: May 25, 2006 1:38 PM .