Reference SNP(refSNP) Cluster Report: rs60834

Reference SNP(refSNP) Cluster Report: rs60834

refSNP ID: rs60834
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:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_003178.4:c.374-28386G>C
NM_133625.3:c.374-28386G>C
NT_022517.17:g.12093765G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44405448 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs60834 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
ss67028	TSC-CSHL\|TSC0055197	fwd/B	C/G	aggaataccctcaaagaaaatagagctgat	aaagaagtggaacaatggggcaggggatag	09/06/00	04/07/04	87	Genomic	95 %
ss395591	KWOK\|OVLP-000621-229847	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	06/30/00	10/10/03	79	Genomic	99 %
ss397100	KWOK\|OVLP-000621-234730	fwd/B	C/G	aggaataccctcaaagaaaatagagctgat	aaagaagtggaacaatggggcaggggatag	06/30/00	10/10/03	87	Genomic	99 %
ss566609	SC_JCM\|AC026166.2_67360	fwd/B	C/G	aggaataccctcaaagaaaatagagctgat	aaagaagtggaacaatggggcaggggatag	07/12/00	10/10/03	87	Genomic	unknown
ss985036	KWOK\|OVLP-000804-603934	fwd/B	C/G	aggaataccctcaaagaaaatagagctgat	aaagaagtggaacaatggggcaggggatag	09/01/00	10/10/03	87	Genomic	99 %
ss985675	KWOK\|OVLP-000804-610091	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	09/01/00	10/10/03	87	Genomic	99 %
ss1614408	KWOK\|OVLP-000925-491414	fwd/B	C/G	aggaataccctcaaagaaaatagagctgat	aaagaagtggaacaatggggcaggggatag	10/04/00	10/10/03	87	Genomic	99 %
ss1615055	KWOK\|OVLP-000925-498017	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	10/04/00	10/10/03	87	Genomic	99 %
ss3732777	SC_JCM\|AC026166.4_103275	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	09/25/01	10/10/03	100	Genomic	unknown
ss5519439	TSC-CSHL\|TSC0547502	fwd/B	C/G	aggaataccctcaaagaaaatagagctgat	aaagaagtggaacaatggggcaggggatag	09/21/02	10/10/03	108	Genomic	unknown
ss5757521	SC_JCM\|NT_005927.12_12083066	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	01/10/03	10/10/03	111	Genomic	unknown
ss16976354	CSHL-HAPMAP\|CSHL-HuAA-200402.chr3.NT_022517.16_12093765	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	02/17/04	03/04/04	120	Genomic	unknown
ss19540479	CSHL-HAPMAP\|CSHL-HuDD-200402.chr3.NT_022517.16_12093765	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	02/20/04	03/04/04	120	Genomic	unknown
ss23207344	PERLEGEN\|afd2334251	rev/T	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	08/10/04	09/13/04	123	Genomic	unknown
ss44405448	ABI\|hCV3114458	rev/	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	07/18/05	11/03/06	126	Genomic	unknown
ss65952182	AFFY\|SNP_A-1709595	fwd/B	C/G	taccctcaaagaaaatagagctgat	aaagaagtggaacaatggggcaggg	10/26/06	10/26/06	127	Genomic	unknown
ss68853118	PERLEGEN\|PGP02334251	rev/	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	01/30/07	08/14/07	127	Genomic	unknown
ss81989460	HGSV\|Cor18956_SNV_20070510.chr3_12128765	rev/	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	11/30/07	12/01/07	130	Genomic	unknown
ss92000321	BCMHGSC_JDW\|JWB-1558518	rev/	C/G	ctatcccctgccccattgttccacttcttt	atcagctctattttctttgagggtattcct	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATACTACATA ATGTGAGAGA TTCTTAGTAC TTTTATATTT TAATGGGTTA ACAGACTTGT
 AACTCCACTG CAAAATTTTT GAAAGCATAC CCTATAGCTG TGGAGGTCTT TGTCTTCCAC
 AGCTATAAGC TGGGTTTGAG TACAGGATAG GCACCCCAAA TAGTGAACCA AACCTAAGTG
 GCCCATGTCA CCGTTCATTT GACAGGGGCA ATTAATCAAT GCTGAATTAA AAAATAAAAT
 TAATTCATTG AATCTGACTG TGAAGTTGCC AGGAATACCC TCAAAGAAAA TAGAGCTGAT
 S
 AAAGAAGTGG AACAATGGGG CAGGGGATAG CAGACAGTCA AACTGTAGCA TGATATTTTA
 CTTGTACACC AGTGCTTTGC TTTCAGATCC CAAGCAGAAG GCTCTTCTAG ACTCAGAGCA
 CTTCTGATAA GCCTCTCCTT AGGTTACACC ACACTCATGT TTTTCAGTGA CAAACACTGC
 TCCCCCTCTT AGCAGAGATT CTAGGGAAAC AAACCATACC AATTCACCCA GGGGTCTCAC
 CTCAGAGTTT CTGCCAATGT CCTAAGAAGT TTCTGAAAGT TGCCTTCCCA GAAGCCTGCT

GeneView

GeneView via analysis of contig annotation: SYN2 synapsin II

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_022517->NM_003178

function

reference

NT_022517->NM_133625

function

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


reference	NT_022517->NM_003178->NP_003169	12093765	forward	intron

reference	NT_022517->NM_133625->NP_598328	12093765	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs60834 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_001838877.2	54180073	12087589	plus	C	alt_assembly_8	HuRef	HuRef	view	300
3	NW_921651.1	12091242	12091242	minus	C	alt_assembly_1	Celera	Celera	view	300
3	NT_022517.17	12093765	12128765	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022517 AC015546 AC022374.1 AC022875 AC022875.2 AC026166.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail						Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C	C/C	C/G	G	G/G	HWP	C	G
ss23207344	AFD_EUR_PANEL	European	46	IG		0.043	0.435		0.522	0.584	0.261	0.739

	AFD_AFR_PANEL	African American	46	IG		0.478	0.391		0.130	0.655	0.674	0.326

	AFD_CHN_PANEL	Asian	48	IG		0.167	0.292		0.542	0.150	0.312	0.688

ss44405448	HapMap-CEU	European	120	IG		0.050	0.267		0.683	0.403	0.183	0.817

	HapMap-HCB	Asian	90	IG		0.022	0.489		0.489	0.100	0.267	0.733

	HapMap-JPT	Asian	88	IG		0.159	0.341		0.500	0.150	0.330	0.670

	HapMap-YRI	Sub-Saharan African	120	IG		0.683	0.267		0.050	0.403	0.817	0.183

	AoD_African_American		90	AF							0.640	0.360

	AoD_Caucasian		92	AF							0.210	0.790

ss67028	AfAm	African American	28	IG		0.571	0.214		0.214	0.100	0.679	0.321

	Caucasian	European	24	IG			0.583		0.417	0.200	0.292	0.708

	Asian	Asian	26	IG		0.308	0.615		0.077	0.294	0.615	0.385

	CEPH	European	54	IG		0.148	0.296		0.556	0.150	0.296	0.704

	PDpanel	Global	16	IG			1.000			0.005	0.500	0.500

	CHMJ	Asian	74	IG	0.784			0.216			0.784	0.216

ss68853118	HapMap-CEU	European	120	GF		0.050	0.267		0.683		0.183	0.817

	HapMap-HCB	Asian	90	GF		0.022	0.489		0.489		0.267	0.733

	HapMap-JPT	Asian	90	GF		0.156	0.356		0.489		0.333	0.667

	HapMap-YRI	Sub-Saharan African	120	GF		0.683	0.267		0.050		0.817	0.183

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss23207344	68	27	26	14
ss44405448	270	109	87	73
ss67028	76	16	34	26
ss68853118	270	109	88	73

RefSNP Genotype Summary	Total Individual	C	C/C	C/G	G	G/G
rs60834	421		146	142		113

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
814	ss67028	C/C	AFFY	Asian	NA17013		AFFY_GENOTYPING_112103
814	ss67028	G/G	AFFY	Asian	NA17013		AFFY_071103
815	ss67028	C/C	AFFY	Asian	NA17014		AFFY_071103
815	ss67028	G/G	AFFY	Asian	NA17014		AFFY_GENOTYPING_112103
833	ss67028	C/C	AFFY	AfAm	NA17102		AFFY_071103
833	ss67028	G/G	AFFY	AfAm	NA17102		AFFY_GENOTYPING_112103
833	ss23207344	G/G	PERLEGEN	AFD_AFR_PANEL	NA17102		71_IND_CHR_3
834	ss67028	C/C	AFFY	AfAm	NA17103		AFFY_071103
834	ss67028	G/G	AFFY	AfAm	NA17103		AFFY_GENOTYPING_112103
834	ss23207344	G/G	PERLEGEN	AFD_AFR_PANEL	NA17103		71_IND_CHR_3
836	ss67028	C/C	AFFY	AfAm	NA17105		AFFY_GENOTYPING_112103
836	ss67028	G/G	AFFY	AfAm	NA17105		AFFY_071103
836	ss23207344	C/C	PERLEGEN	AFD_AFR_PANEL	NA17105		71_IND_CHR_3
897	ss67028	C/C	AFFY	Caucasian	NA17202		AFFY_GENOTYPING_112103
897	ss67028	G/G	AFFY	Caucasian	NA17202		AFFY_071103
898	ss67028	C/C	AFFY	Caucasian	NA17203		AFFY_GENOTYPING_112103
898	ss67028	G/G	AFFY	Caucasian	NA17203		AFFY_071103
900	ss67028	C/C	AFFY	Caucasian	NA17205		AFFY_GENOTYPING_112103
900	ss67028	G/G	AFFY	Caucasian	NA17205		AFFY_071103
901	ss67028	C/C	AFFY	Caucasian	NA17206		AFFY_GENOTYPING_112103
901	ss67028	G/G	AFFY	Caucasian	NA17206		AFFY_071103
904	ss67028	C/C	AFFY	Caucasian	NA17210		AFFY_071103
904	ss67028	G/G	AFFY	Caucasian	NA17210		AFFY_GENOTYPING_112103
905	ss67028	C/C	AFFY	Caucasian	NA17211		AFFY_GENOTYPING_112103
905	ss67028	G/G	AFFY	Caucasian	NA17211		AFFY_071103
906	ss67028	C/C	AFFY	Caucasian	NA17212		AFFY_GENOTYPING_112103
906	ss67028	G/G	AFFY	Caucasian	NA17212		AFFY_071103
1208	ss67028	C/C	AFFY	PDpanel	PD01		AFFY_GENOTYPING_112103
1208	ss67028	G/G	AFFY	PDpanel	PD1		AFFY_071103
1214	ss67028	C/C	AFFY	PDpanel	PD07		AFFY_GENOTYPING_112103
1214	ss67028	G/G	AFFY	PDpanel	PD7		AFFY_071103
1215	ss67028	C/C	AFFY	PDpanel	PD08		AFFY_GENOTYPING_112103
1215	ss67028	G/G	AFFY	PDpanel	PD8		AFFY_071103
1216	ss67028	C/C	AFFY	PDpanel	PD09		AFFY_GENOTYPING_112103
1216	ss67028	G/G	AFFY	PDpanel	PD9		AFFY_071103
1218	ss67028	C/C	AFFY	PDpanel	PD11		AFFY_071103
1218	ss67028	G/G	AFFY	PDpanel	PD11		AFFY_GENOTYPING_112103
1219	ss67028	C/C	AFFY	PDpanel	PD12		AFFY_GENOTYPING_112103
1219	ss67028	G/G	AFFY	PDpanel	PD12		AFFY_071103
1220	ss67028	C/C	AFFY	PDpanel	PD13		AFFY_GENOTYPING_112103
1220	ss67028	G/G	AFFY	PDpanel	PD13		AFFY_071103
1221	ss67028	C/C	AFFY	PDpanel	PD14		AFFY_GENOTYPING_112103
1221	ss67028	G/G	AFFY	PDpanel	PD14		AFFY_071103
1223	ss67028	C/C	AFFY	PDpanel	PD16		AFFY_GENOTYPING_112103
1223	ss67028	G/G	AFFY	PDpanel	PD16		AFFY_071103
1224	ss67028	C/C	AFFY	PDpanel	PD17		AFFY_GENOTYPING_112103
1224	ss67028	G/G	AFFY	PDpanel	PD17		AFFY_071103
1225	ss67028	C/C	AFFY	PDpanel	PD18		AFFY_071103
1225	ss67028	G/G	AFFY	PDpanel	PD18		AFFY_GENOTYPING_112103
1226	ss67028	C/C	AFFY	PDpanel	PD19		AFFY_GENOTYPING_112103
1226	ss67028	G/G	AFFY	PDpanel	PD19		AFFY_071103
1227	ss67028	C/C	AFFY	PDpanel	PD20		AFFY_GENOTYPING_112103
1227	ss67028	G/G	AFFY	PDpanel	PD20		AFFY_071103
1228	ss67028	C/C	AFFY	PDpanel	PD21		AFFY_071103
1228	ss67028	G/G	AFFY	PDpanel	PD21		AFFY_GENOTYPING_112103
1230	ss67028	C/C	AFFY	PDpanel	PD23		AFFY_GENOTYPING_112103
1230	ss67028	G/G	AFFY	PDpanel	PD23		AFFY_071103
1231	ss67028	C/C	AFFY	PDpanel	PD24		AFFY_GENOTYPING_112103
1231	ss67028	G/G	AFFY	PDpanel	PD24		AFFY_071103

Genotype data submitted for	454	samples from	421	individuals	Individual with multiple genotypes submission:	291

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .