Reference SNP(refSNP) Cluster Report: rs264827

Reference SNP(refSNP) Cluster Report: rs264827

refSNP ID: rs264827
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/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_004946.1:c.844-600A>G
NT_023133.12:g.13931765A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1620657 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs264827 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
ss345062	KWOK\|OVLP-000621-100230	rev/B	C/T	gggctctgattacttacttactctgggccc	tggctggcagctctgtctcagcacgggtgc	06/30/00	10/10/03	79	Genomic	99 %
ss496584	SC_JCM\|AC023084.2_1020	rev/B	C/T	gggctctgattacttacttactctgggccc	tggctggcagctctgtctcagcacgggtgc	07/12/00	10/10/03	80	Genomic	unknown
ss1073493	KWOK\|OVLP-000804-25540	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	09/02/00	10/10/03	86	Genomic	99 %
ss1332032	TSC-CSHL\|TSC0176227	rev/B	C/T	gggctctgattacttacttactctgggccc	tggctggcagctctgtctcagcacgggtgc	09/06/00	10/10/03	86	Genomic	95 %
ss1620657	KWOK\|OVLP-000925-555081	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	10/04/00	05/16/04	87	Genomic	99 %
ss11721519	WI_SSAHASNP\|chr5.NT_023133.11_13931765	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	07/03/03	10/10/03	116	Genomic	unknown
ss19637181	CSHL-HAPMAP\|CSHL-HuDD-200402.chr5.NT_023133.11_13931765	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	02/20/04	03/04/04	120	Genomic	unknown
ss42541475	ABI\|hCV1949902	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	07/18/05	07/18/05	126	Genomic	unknown
ss67265482	ILLUMINA\|HumanHap550v1.1_rs264827	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	11/14/06	11/14/06	127	Genomic	unknown
ss67665319	ILLUMINA\|HumanHap650Yv1.0_rs264827	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	11/14/06	11/14/06	127	Genomic	unknown
ss68209151	ILLUMINA\|HumanHap250Sv1.0_rs264827	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	12/06/06	12/07/06	127	Genomic	unknown
ss68958325	PERLEGEN\|PGP07995900	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	01/30/07	08/14/07	127	Genomic	unknown
ss70743882	ILLUMINA\|HumanHap550v3.0__rs264827	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	04/20/07	03/30/08	130	Genomic	unknown
ss71315280	ILLUMINA\|HumanHap650Yv3.0_rs264827	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	04/23/07	04/23/07	127	Genomic	unknown
ss75636005	ILLUMINA\|ILMN_Human_1M_rs264827	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	08/28/07	08/29/07	129	Genomic	unknown
ss78117311	HGSV\|Cor12878_SNV_20070510.chr5_169054785	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	10/17/07	10/17/07	129	Genomic	unknown
ss83406880	KRIBB_YJKIM\|KHS454216	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	12/04/07	12/05/07	130	Genomic	unknown
ss84546691	HGSV\|Cor19129_SNV_20070510.chr5_169054785	fwd/T	A/G	gcacccgtgctgagacagagctgccagcca	gggcccagagtaagtaagtaatcagagccc	12/06/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 TCTGATGCCA ACAGCATGTC TTGTTGTTTC TTCCTTAGCT GATCCTTACT GGCAGGGGGC
 CTCAAGATCA CTGAAGCTTT TAGATTCGAG CATGAAGTCA GGAGTTTCCT CCTGCATGCC
 TTTCTGATGG CAAGGGAGCT GTACTGtagt agctatgttt gtggtctttg gtgtcaggga
 ctgggctcaa agcccagagt ctcatgggct atggtcatga ccttggggaa gcctcttatc
 ttctttgtgt ctcagtttcc ccatctgtca aatggggatg caataattgt atgtacttca
 gagatgtgag agattgaata tggtgatgca ggaatcactt agcacagtgG ATGAGAGTGC
 GTTTCACCAG TTTTGGCTTT TCTAGACTCA GTTGagctgg gtctggtggc tcatgtctgt
 aatcccagca ctttcggagg ctgatgtggg aggattgctt gagcccagga gtttgaaatc
 agcctggaca acatagtgag accccatctc ttaaaaaaaa aattaggtag gcatggtggc
 tcatgcctgt agtcccagct actcaagagg ctgaggtggg aggattattt gagcctggga
 gactgaggct gcagtgagct gtgatcatgc tactgccctc tagcctgtgt gacagagtga
 agccctgtct caaaataaat aaaataaata aataaacaaa cagataGTTG ACTGCAgttt
 cctgacccct tgaagtcagg tgcggccata tgcctttctt tggcaaatga catgcaagca
 aaaagtgatg tgcATCTCTC TTGGGTAGAT GATTTAAAAG CCAGAAGTGA TTTGCCACAT
 TCCTTTCCCC TGTGGCAGAG ACAGTGAGCG CACCCGTGCT GAGACAGAGC TGCCAGCCA
 R
 GGGCCCAGAG TAAGTAAGTA ATCAGAGCCC CCACCCCTCT GCATTGGCCC TGTAGACTGC
 ACCAGAAGTA AACTTCTGCT GTGTTGTAAG CACTGAGATA TTGGGGTTGT TAGCACTACC
 TCAACCCAAC TGATGGCCAC ACTTTAGATG TGCAGGAAAT GGTAGCTGTT ATGATTTTTT
 TCTCTTCCTT TTGTCTTCTC TCTCAGAGGT TCTGAGCAAT GATGTGACCG ATGGTGTCAT
 CCGAGTCATC TGTAGCAAAT GCTACTTTTG GATCTATCAC CTCGGCATAT GGGGAATCCT
 GTCTGTACAG C

GeneView

GeneView via analysis of contig annotation: DOCK2 dedicator of cytokinesis 2

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_023133->NM_004946

function

HuRef

NW_001838954->NM_004946

function

Celera

NW_922784->NM_004946

function

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


reference	NT_023133->NM_004946->NP_004937	13931765	forward	intron

HuRef	NW_001838954->NM_004946->NP_004937	6241591	reverse	intron

Celera	NW_922784->NM_004946->NP_004937	42781823	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs264827 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838954.2	6241591	164220734	minus	T	alt_assembly_8	HuRef	HuRef	view	899
5	NW_922784.1	42781823	165153807	plus	A	alt_assembly_1	Celera	Celera	view	899
5	NT_023133.12	13931765	169054785	plus	A	ref_assembly	reference	reference	view	899

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023133 AC008680 AC023084.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1620657	CEPH		184	AF					0.600	0.400

	HapMap-CEU	European	118	IG	0.525	0.390	0.085	1.000	0.720	0.280

	HapMap-HCB	Asian	90	IG	0.711	0.244	0.044	0.439	0.833	0.167

	HapMap-JPT	Asian	90	IG	0.400	0.467	0.133		0.633	0.367

	HapMap-YRI	Sub-Saharan African	120	IG	0.050	0.083	0.867	0.001	0.092	0.908

ss68958325	HapMap-CEU	European	120	GF	0.533	0.383	0.083		0.725	0.275

	HapMap-HCB	Asian	90	GF	0.622	0.333	0.044		0.789	0.211

	HapMap-JPT	Asian	90	GF	0.400	0.467	0.133		0.633	0.367

	HapMap-YRI	Sub-Saharan African	120	GF	0.050	0.083	0.867		0.092	0.908

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss1620657	264	94	79	90
ss68958325	264	95	79	90

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs264827	270	95	79	90

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5150	ss1620657	A/A	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	r23_ch5_HCB_perlegen:genotyping_1.0.0	3003174
5150	ss68958325	A/G	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	chr5-HapMap-HCB
5153	ss1620657	A/A	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	r23_ch5_HCB_perlegen:genotyping_1.0.0	3003174
5153	ss68958325	A/G	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	chr5-HapMap-HCB
5169	ss1620657	A/A	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	r23_ch5_HCB_perlegen:genotyping_1.0.0	3003174
5169	ss68958325	A/G	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	chr5-HapMap-HCB
5174	ss1620657	A/A	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r23_ch5_HCB_perlegen:genotyping_1.0.0	3003174
5174	ss68958325	A/G	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	chr5-HapMap-HCB
5191	ss1620657	A/G	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	r23_ch5_HCB_perlegen:genotyping_1.0.0	3003174
5191	ss68958325	A/A	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	chr5-HapMap-HCB
5192	ss1620657	A/A	CSHL-HAPMAP	HapMap-HCB	NA18637	CH18637	r23_ch5_HCB_perlegen:genotyping_1.0.0	3003174
5192	ss68958325	A/G	CSHL-HAPMAP	HapMap-HCB	NA18637	CH18637	chr5-HapMap-HCB

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

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 .