Reference SNP(refSNP) Cluster Report: rs800167

Reference SNP(refSNP) Cluster Report: rs800167

refSNP ID: rs800167
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:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_018448.2:c.69-1786G>A
NT_029419.11:g.29817210G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5271508 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs800167 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
ss1006551	KWOK\|OVLP-000804-140026	fwd/B	C/T	gcattggggcaatacaagatcagttaagca	gtacttttaaaaaatggacacagctctcct	09/02/00	10/10/03	86	Genomic	97 %
ss1907125	KWOK\|OVLP-000925-459206	fwd/B	C/T	gcattagggcaatacaagatcagttaagca	gtacttttaaaaaatggacacagctctcct	10/06/00	10/10/03	87	Genomic	99 %
ss1957335	KWOK\|OVLP-000925-460528	fwd/B	C/T	gcattggggcaatacaagatcagttaagca	gtacttttaaaaaatggacacagctctcct	10/06/00	10/10/03	87	Genomic	97 %
ss2573117	SC_JCM\|AC078879.5_12925	fwd/B	C/T	gcattagggcaatacaagatcagttaagca	gtacttttaaaaaatggacacagctctcct	11/03/00	10/10/03	92	Genomic	unknown
ss5271508	TSC-CSHL\|TSC1720828	fwd/B	C/T	gcattagggcaatacaagatcagttaagca	gtacttttaaaaaatggacacagctctcct	09/20/02	04/07/04	108	Genomic	unknown
ss15667836	SC_SNP\|NT_029419.10_29817210	rev/T	A/G	aggagagctgtgtccattttttaaaagtac	tgcttaactgatcttgtattgccctaatgc	11/17/03	11/22/03	120	Genomic	unknown
ss19246796	CSHL-HAPMAP\|CSHL-HuDD-200402.chr12.NT_029419.10_29817210	rev/T	A/G	aggagagctgtgtccattttttaaaagtac	tgcttaactgatcttgtattgccctaatgc	02/20/04	03/04/04	120	Genomic	unknown
ss20916455	SSAHASNP\|WGSA-200403-chr12.chr12.NT_029419.10_29817210	rev/T	A/G	aggagagctgtgtccattttttaaaagtac	tgcttaactgatcttgtattgccctaatgc	03/19/04	03/19/04	121	Genomic	unknown
ss38916694	ABI\|hCV3229754	rev/T	A/G	aggagagctgtgtccattttttaaaagtac	tgcttaactgatcttgtattgccccaatgc	07/16/05	11/02/06	126	Genomic	unknown
ss65990194	AFFY\|SNP_A-1741534	fwd/B	C/T	agggcaatacaagatcagttaagca	gtacttttaaaaaatggacacagct	10/26/06	10/26/06	127	Genomic	unknown
ss81397928	HGSV\|Cor18507_SNV_20070510.chr12_65960171	rev/T	A/G	aggagagctgtgtccattttttaaaagtac	tgcttaactgatcttgtattgccctaatgc	11/26/07	11/29/07	130	Genomic	unknown
ss85298373	HGSV\|Cor18517_SNV_20070510.chr12_65960171	rev/T	A/G	aggagagctgtgtccattttttaaaagtac	tgcttaactgatcttgtattgccctaatgc	12/06/07	12/08/07	130	Genomic	unknown
ss89219552	BCMHGSC_JDW\|JWB-0574036	rev/T	A/G	aggagagctgtgtccattttttaaaagtac	tgcttaactgatcttgtattgccctaatgc	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 AAAGTCAAAT GAACTTGTCC CATAATTCTT GGCTCCCCTC CACTTACAGA AGCAATCCAA
 CTAAGATAAC TAGTTAACAC TTTTTTCTTT TATTTGAACC AGATACAGTT TTAGTAAAAA
 TACGTTATTT TGTACACTAC AGAGAAATGT CAAAATCCAT GTTTAAACAA AAAAACAACT
 ATTGGAGCTG AATTGATAAA CAGCTATGGA GATAGTCCGC AACATGGGAA ATAAACTGTG
 TGGTAAAGGT TGGCAAAACA ACTTAATAAT TTAGAAATGC ATTACATGTA AGGCAATTTT
 AAGGATAATT CCAATAACTA GTACGTTCAT TTAATGCTGA TCTGACAAAG TTTTACACTA
 CATGCAAGTA GGTATTatgg taaaaaccac aattactttt gcaccaacct aaTAGTTTAA
 TTCTTACCAC GTTCTGTAAA ACTGCTTATT TTTAAAAAAG CTTATATTTG CATTAGGGCA
 ATACAAGATC AGTTAAGCA
 Y
 GTACTTTTAA AAAATGGACA CAGCTCTCCT AATTGGAAGC CCCTCACCCA TTTTATAATG
 TGACAAAACA AAATTAAAAC TACATGACTA ATTTTCATTA ATATTCTGGA AAGTGGAAAA
 ATTGCATAAC ACATTAATGC AGGCACTCCT GCACACAAAG TACTGAAAAA ATCTTAACTG
 TTTTACTTAA ACAAAATCCA TTAAATAACC ATAATAGTTA TGACCTCTAA GAACCACTGC
 AGTGCCAGTT ACCTGCTTCC AGAGAAAACA GGGATCATCA ATTTAAGTAG AAAAACATAA
 TCCCAAGTAA AAAGTTGTTT TATGGTCCTG TATGGTTCTA CCGGCACAAA TTCATTCTTT
 ACTTATTGTT TATTTATTCA CTGTCTATTA TGTAAGAAAC TCTGGACTAA GAAATCAGGA
 CAGATAAAAG TTGAATACAC TTTGGCCCCC CTAACATCAA GAAGCTTACT TATATTGTAA
 TAAAGAAGCC TACTGATTTT

GeneView

GeneView via analysis of contig annotation: CAND1 cullin-associated and neddylation-dissociated 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_029419->NM_018448

function

HuRef

NW_001838060->NM_018448

function

Celera

NW_925395->NM_018448

function

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


reference	NT_029419->NM_018448->NP_060918	29817210	forward	intron

HuRef	NW_001838060->NM_018448->NP_060918	8841889	reverse	intron

Celera	NW_925395->NM_018448->NP_060918	14961742	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs800167 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838060.2	8841889	64724688	plus	C	alt_assembly_8	HuRef	HuRef	view	499
12	NT_029419.11	29817210	65960171	minus	G	ref_assembly	reference	reference	view	499
12	NW_925395.1	14961742	67337913	minus	A	alt_assembly_1	Celera	Celera	view	499

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029419 AC012385 AC012518 AC026491 AC026491.3 AC078879.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC012518.19 NC_000012.10	AC026491.3 AC078879.7

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss38916694	AoD_African_American		90	AF					0.060	0.940

	AoD_Caucasian		92	AF					0.190	0.810

ss5271508	AfAm	African American	12	IG		0.333	0.667	0.655	0.167	0.833

	Caucasian	European	24	IG		0.417	0.583	0.371	0.208	0.792

	Asian	Asian	12	IG	0.333	0.333	0.333	0.439	0.500	0.500

	CEPH	European	12	IG			1.000			1.000

	PDpanel	Global	48	IG	0.208	0.417	0.375	0.527	0.417	0.583

	HapMap-CEU	European	120	IG	0.050	0.417	0.533	0.527	0.258	0.742

	HapMap-HCB	Asian	90	IG	0.267	0.511	0.222	1.000	0.522	0.478

	HapMap-JPT	Asian	88	IG	0.432	0.477	0.091	1.000	0.670	0.330

	HapMap-YRI	Sub-Saharan African	120	IG		0.117	0.883	0.752	0.058	0.942

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.447+/-0.155	324	263	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .