Reference SNP(refSNP) Cluster Report: rs723606

Reference SNP(refSNP) Cluster Report: rs723606

refSNP ID: rs723606
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:	C
Clinical Association:	unknown

HGVS Names
NM_020923.1:c.189-1278G>A
NT_005403.16:g.57377580G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss84265970 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs723606 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
ss65892	TSC-CSHL\|TSC0053387	fwd/B	C/T	tgatattgccatggcctgaattcttaaagt	gggcaaacattcattcatgtaacaaccatc	09/06/00	04/07/04	86	Genomic	95 %
ss44199387	ABI\|hCV1282717	rev/T	A/G	gatggttgttacatgaatgaatgtttgccc	actttaagaattcaggccatggcaatatca	07/18/05	11/03/06	126	Genomic	unknown
ss65719616	ILLUMINA\|Human1-rs723606	fwd/B	C/T	tgatattgccatggcctgaattcttaaagt	gggcaaacattcattcatgtaacaaccatc	10/10/06	10/10/06	127	Genomic	unknown
ss65948418	AFFY\|SNP_A-1697655	rev/T	A/G	ttgttacatgaatgaatgtttgccc	actttaagaattcaggccatggcaa	10/26/06	10/26/06	127	Genomic	unknown
ss66504721	AFFY\|SNP_A-4208634	rev/T	A/G	gaatgaatgtttgccc	actttaagaattcagg	10/29/06	10/29/06	127	Genomic	unknown
ss67937210	ILLUMINA\|HumanHap650Yv1.0_rs723606	fwd/B	C/T	tgatattgccatggcctgaattcttaaagt	gggcaaacattcattcatgtaacaaccatc	11/14/06	11/15/06	127	Genomic	unknown
ss71517521	ILLUMINA\|HumanHap650Yv3.0_rs723606	fwd/B	C/T	tgatattgccatggcctgaattcttaaagt	gggcaaacattcattcatgtaacaaccatc	04/23/07	04/23/07	127	Genomic	unknown
ss75347317	ILLUMINA\|ILMN_Human_1M_rs723606	fwd/B	C/T	tgatattgccatggcctgaattcttaaagt	gggcaaacattcattcatgtaacaaccatc	08/28/07	08/29/07	129	Genomic	unknown
ss76327605	AFFY\|AFFY_6_1M_SNP_A-4208634	rev/T	A/G	gaatgaatgtttgccc	actttaagaattcagg	08/28/07	08/30/07	130	Genomic	unknown
ss84265970	HGSV\|Cor19240_SNV_20070510.chr2_206993669	rev/T	A/G	gatggttgttacatgaatgaatgtttgccc	actttaagaattcaggccatggcaatatca	11/30/07	12/06/07	130	Genomic	unknown
ss91520831	BCMHGSC_JDW\|JWB-1373635	rev/T	A/G	gatggttgttacatgaatgaatgtttgccc	actttaagaattcaggccatggcaatatca	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATGTATATGT ATTTCCCATT CAAAATTTAA ATTCCATTAT TTTTAAAAAG ACCCAAAACT
 TTCATATCTA AAATCAGTCT ATGAATCTCT TCTACCAGTA TCAAGACAAC ATGTTTGACC
 AAAGCATTTC AGGGACTGTT CTTTCATGTA CATAAAACCA ACTGACCTAA TGATATTGCC
 ATGGCCTGAA TTCTTAAAGT
 Y
 GGGCAAACAT TCATTCATGT AACAACCATC TACTAAGGAC TTACTACTGC ATTACAGGCA
 CTATGCTAGG TACTAAGGCA AATTCAAAAA AAGTTAAGCT GCCTTTTAAA GACCATTCAA
 GTAGCTGCAG AAGGCAGACA CATAAAAAAT AATAACAATT CAAAGAGATA AGTATCATCA
 CATCTAGACC TGTTTAAAAA AAAAAAAAAA AAGATTAAAC TGTCACAGCC AAGAGGGACC
 TAAAGAGACA TTACAAGTTA ATGTAATGTG GTATCCTGGA TGTGATTCTG AAACAGAAAA
 AGTAGTAAAA CTAAGGAAAT CTTAGTTTAA GAAAACTTAG TTTAAGTAGA AACTAAGAAG
 TCTGAATAAA CCATGGACTG TACTAATATC AGTTCATTAC TTATAACAAA TATATCACAT
 TAATGTTAAT AATAGAGAAA TTGTGTGAGA GAGTATTATA GGCACACTCT GTACTATTTC
 CTCATTGTTT CCATTAATCT

GeneView

GeneView via analysis of contig annotation: ZDBF2 zinc finger, DBF-type containing 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_005403->NM_020923

function

HuRef

NW_001838863->NM_020923

function

Celera

NW_921618->NM_020923

function

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


reference	NT_005403->NM_020923->NP_065974	57377580	forward	intron

HuRef	NW_001838863->NM_020923->NP_065974	32574490	forward	intron

Celera	NW_921618->NM_020923->NP_065974	11844545	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs723606 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838863.1	32574490	199018184	minus	A	alt_assembly_8	HuRef	HuRef	view	300
2	NW_921618.1	11844545	200930015	minus	G	alt_assembly_1	Celera	Celera	view	300
2	NT_005403.16	57377580	206876408	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
AC017081.5

dbSNP Blast Analysis
GenBank HTGS Finished:
AC017081.8 NC_000002.10

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	A	C	G	T
ss44199387	HapMap-CEU	European	120	IG			0.233	0.483		0.283	1.000		0.475		0.525

	HapMap-HCB	Asian	90	IG			0.622	0.356		0.022	0.479		0.800		0.200

	HapMap-JPT	Asian	88	IG			0.682	0.295		0.023	1.000		0.830		0.170

	HapMap-YRI	Sub-Saharan African	120	IG			0.533	0.400		0.067	1.000		0.733		0.267

ss65892	TSC_42_AA		82	AF									0.650		0.350

	TSC_42_C		76	AF									0.500		0.500

	TSC_42_A		82	AF									0.870		0.130

	AfAm	African American	40	IG	0.100	0.400			0.500		1.000	0.300		0.700

	Caucasian	European	40	IG	0.350	0.350			0.300		0.200	0.525		0.475

	Asian	Asian	40	IG		0.300			0.700		0.439	0.150		0.850

	CEPH	European	46	IG	0.435	0.348			0.217		0.200	0.609		0.391

	PDpanel	Global	48	IG	0.167	0.333			0.500		0.251	0.333		0.667

Concordant Genotype	Total Sample	A/A	A/G	C/C	C/T	G/G	T/T
ss44199387	267	30	109			127
ss65892	105	21	37			47

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs723606	375	51	146			174

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
215	ss65892	A/A	AFFY	CEPH	NA10857		AFFY_071103
215	ss44199387	A/A	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r23_ch2_CEU_illumina:golden_gate_1.0.0	288208
225	ss65892	A/A	AFFY	CEPH	NA12043		AFFY_071103
225	ss44199387	A/A	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r23_ch2_CEU_illumina:golden_gate_1.0.0	288208
226	ss65892	A/A	AFFY	CEPH	NA12044		AFFY_071103
226	ss44199387	A/A	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r23_ch2_CEU_illumina:golden_gate_1.0.0	288208

Genotype data submitted for	384	samples from	375	individuals	Individual with multiple genotypes submission:	9

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .