Reference SNP(refSNP) Cluster Report: rs486706

Reference SNP(refSNP) Cluster Report: rs486706

refSNP ID: rs486706
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_021080.3:c.307-4696C>T
NT_032977.8:g.27514702G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1937419 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs486706 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
ss656372	SC_JCM\|AL138779.5_51277	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	07/27/00	10/10/03	83	Genomic	unknown
ss1937419	KWOK\|OVLP-000925-745587	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	10/06/00	10/25/06	87	Genomic	99 %
ss2595065	SC_JCM\|AL138779.7_45613	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	11/03/00	10/10/03	89	Genomic	unknown
ss6789236	WI_SSAHASNP\|NT_029223.9_769911	rev/T	A/G	atgggcgaagggcatcaaagaaggcttgac	aagggggtgaccttgaattgaggctccaag	02/12/03	10/10/03	111	Genomic	unknown
ss9856156	BCM_SSAHASNP\|chr1.NT_032977.5_9991695	rev/T	A/G	atgggcgaagggcatcaaagaaggcttgac	aagggggtgaccttgaattgaggctccaag	06/27/03	10/10/03	116	Genomic	unknown
ss11385670	WI_SSAHASNP\|chr1.NT_032977.5_9991695	rev/T	A/G	atgggcgaagggcatcaaagaaggcttgac	aagggggtgaccttgaattgaggctccaag	07/03/03	10/10/03	116	Genomic	unknown
ss16434382	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_032977.6_19105854	rev/T	A/G	atgggcgaagggcatcaaagaaggcttgac	aagggggtgaccttgaattgaggctccaag	02/17/04	03/04/04	120	Genomic	unknown
ss20531272	SSAHASNP\|WGSA-200403-chr1.chr1.NT_032977.6_19105854	rev/T	A/G	atgggcgaagggcatcaaagaaggcttgac	aagggggtgaccttgaattgaggctccaag	03/18/04	03/18/04	121	Genomic	unknown
ss67390048	ILLUMINA\|HumanHap550v1.1_rs486706	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	11/14/06	11/14/06	127	Genomic	unknown
ss67764151	ILLUMINA\|HumanHap650Yv1.0_rs486706	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	11/14/06	11/14/06	127	Genomic	unknown
ss68238916	ILLUMINA\|HumanHap250Sv1.0_rs486706	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	12/06/06	12/07/06	127	Genomic	unknown
ss68766876	PERLEGEN\|PGP06558986	rev/T	A/G	atgggcgaagggcatcaaagaaggcttgac	aagggggtgaccttgaattgaggctccaag	01/30/07	08/14/07	127	Genomic	unknown
ss70831698	ILLUMINA\|HumanHap550v3.0__rs486706	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	04/20/07	03/31/08	130	Genomic	unknown
ss71414415	ILLUMINA\|HumanHap650Yv3.0_rs486706	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	04/23/07	04/23/07	127	Genomic	unknown
ss75534971	ILLUMINA\|ILMN_Human_1M_rs486706	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	08/28/07	08/29/07	129	Genomic	unknown
ss76487217	AFFY\|AFFY_6_1M_SNP_A-8348233	rev/T	A/G	tcaaagaaggcttgac	aagggggtgaccttga	08/28/07	08/30/07	129	Genomic	unknown
ss83464705	KRIBB_YJKIM\|KHS467737	fwd/B	C/T	cttggagcctcaattcaaggtcaccccctt	gtcaagccttctttgatgcccttcgcccat	12/04/07	12/05/07	130	Genomic	unknown
ss87451098	BCMHGSC_JDW\|JWB-0049664	rev/T	A/G	atgggcgaagggcatcaaagaaggcttgac	aagggggtgaccttgaattgaggctccaag	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 GTTCTCTGTT CGCAGAATGA ATCGCTGTGT GAAATGTTAT GAATTAACCT GAATCATTTA
 TTCATTGAAC ATGTATTGAG CATCGCGCCA TATGTAGGGC TTATCTTAAG GTGACTTGGT
 CTTTCGGTCT TTTCTTCCTC CCCATTCATT TCCTTCATCC AGGACTTCCT TTCTTTCTTC
 CTCCCTGCCT GCCTTCCTGA AATATTATGT AACACTTACT GTTCAGAAGG TGCAGTATTA
 GGAGCGGGGG TAAGATTGAG AAGAACCAGA CATGGATCTT TCTCTGAAGG GCCTAACATT
 CCTGAAGGAG AGAGAGAAAA CATGTGCATA GATGTTCTCC ACAAGGTCCT GTTCTCAGAA
 CCTAGCTgcc ttcacacatt cagttctttc tgcctaaaat gccctttctt ccttattttc
 tggagacttc ccatctatcc ttggagcctc aattcaaggt caccccctt
 Y
 gtcaagcctt ctttgatgcc cttcgcccat tcctgcccca agcctatgtg acacactggg
 cacactttta atataaagct tgttgtatta tattgtgatt gctagtttct ttgcctacct
 gttttatgag attgtgaact ccttgaagaa gggactgtgt tttattcatc tgtgtagcca
 tagcacatag caggagacca gcaacataat aggcactcaa taagtACACA TGCTGTGAGT
 AACTGGATGA ATGGATAAAT GCGAAAGAAG TGCAAAGCAT CCTGTGTAGA AGGACAAATA
 TAATGCAGTG AGATCTAGGG ATGGGAATTA TTACTCAGGG AAAtggggta tcaaggtagg
 ttccttggat gggcaacatg tcagagctat gccttccgtc ataggtacac tatagttctc
 tgagctgatg aagcgcaggc cagggcatct gcagagaaaa ccatgtgagc aatagcacag
 aagtgggaaa gCACAAAATT CAAAGGGAGA GTAATGAGCT CCTCAGATTA TTTGCAGCAC
 AGGTGACCTG AAGTTCATGC ATAGGAAGGT CAGATTGGAT TGAGGACATT G

GeneView

GeneView via analysis of contig annotation: DAB1 disabled homolog 1 (Drosophila)

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_032977->NM_021080

function

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


reference	NT_032977->NM_021080->NP_066566	27514702	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs486706 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838579.2	26139174	55655548	plus	T	alt_assembly_8	HuRef	HuRef	view	469
1	NW_921351.1	31688473	55827615	minus	A	alt_assembly_1	Celera	Celera	view	469
1	NT_032977.8	27514702	57315371	minus	G	ref_assembly	reference	reference	view	469

NCBI Resource Links

Submitter-Referenced
GenBank
NT_032977 AL354883 AL354883.7

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL354883.14	AL138779.7

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1937419	HapMap-CEU	European	120	IG	0.017	0.267	0.717	0.752	0.150	0.850

	HapMap-HCB	Asian	90	IG		0.178	0.822	0.527	0.089	0.911

	HapMap-JPT	Asian	90	IG		0.089	0.911	1.000	0.044	0.956

	HapMap-YRI	Sub-Saharan African	120	IG			1.000			1.000

ss68766876	HapMap-CEU	European	120	GF	0.017	0.267	0.717		0.150	0.850

	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

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.133+/-0.221	270	210	270	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 .