Reference SNP(refSNP) Cluster Report: rs6855192

Reference SNP(refSNP) Cluster Report: rs6855192

refSNP ID: rs6855192
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
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_133477.1:c.106-51706C>T
NT_016354.18:g.44441024C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss92747627 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6855192 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
ss10182481	BCM_SSAHASNP\|chr4.NT_016354.15_44388008	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	06/27/03	10/25/06	116	Genomic	unknown
ss14596633	WI_SSAHASNP\|chr4.NT_016354.16_44388008	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	11/05/03	11/22/03	119	Genomic	unknown
ss23280577	PERLEGEN\|afd3522555	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	08/10/04	09/13/04	123	Genomic	unknown
ss67508440	ILLUMINA\|HumanHap550v1.1_rs6855192	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	11/14/06	11/14/06	127	Genomic	unknown
ss67871643	ILLUMINA\|HumanHap650Yv1.0_rs6855192	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	11/14/06	11/14/06	127	Genomic	unknown
ss68261807	ILLUMINA\|HumanHap250Sv1.0_rs6855192	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	12/06/06	12/07/06	127	Genomic	unknown
ss68909400	PERLEGEN\|PGP03522555	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	01/30/07	03/31/08	127	Genomic	unknown
ss70891588	ILLUMINA\|HumanHap550v3.0__rs6855192	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	04/20/07	03/31/08	130	Genomic	unknown
ss71484657	ILLUMINA\|HumanHap650Yv3.0_rs6855192	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	04/23/07	04/23/07	127	Genomic	unknown
ss74824256	AFFY\|SNP_M-579720	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	08/09/07	08/09/07	128	Genomic	unknown
ss75461956	ILLUMINA\|ILMN_Human_1M_rs6855192	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	08/28/07	08/29/07	129	Genomic	unknown
ss76546773	AFFY\|AFFY_6_1M_SNP_A-8407879	fwd/B	C/T	ggcagtaagagaaaga	ctggccagcttttcct	08/28/07	08/30/07	129	Genomic	unknown
ss78458937	HGSV\|Cor12878_SNV_20070510.chr4_120250482	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	10/17/07	10/19/07	129	Genomic	unknown
ss84562496	KRIBB_YJKIM\|KHS744454	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	12/04/07	12/07/07	130	Genomic	unknown
ss92747627	BCMHGSC_JDW\|JWB-1842158	fwd/B	C/T	acacagtggtctgaggcagtaagagaaaga	ctggccagcttttccttttcaatgcagtaa	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 ACAATGTGAC TTAGACCTGA GGCTAGAATG GCGCTTCCAT ATCTTTTAGG AATTAATGTT
 TATTACATTA AAGCCAATGG GTCTCCAGTG AAAGGGCAAC CTGACTTATT CATTCATAGA
 CAGCAAAGCT GGCCTGGAGA ACAAAAGCTA GCTGGGCCTG CTAGGGCAGG GTTTGCCTAC
 TTTCTGGGTC CTGAAGCACA AGTGAGCGCA TCATCTGTGA ACACAGTGGT CTGAGGCAGT
 AAGAGAAAGA
 Y
 CTGGCCAGCT TTTCCTTTTC AATGCAGTAA CCATGGTCTC TGAAAAATAA TGGCTCAATG
 ACTCAGTCTC TCTTTAATCA AATTAGCTAC TCTTCCCATG CCGAGAAGTG ACAGGAGAGA
 TCCAGAAGTG TTATGTTCTC CCATCCATGA GAGGGGTGGA CATTCCCTCT TTTGAGAAAG
 TGTAAGAAGG AAAATAATGG TTTCTTCAAC ATCACATAAT TCTACAGGGA TAGACCTCAT
 AGTGTGGTCC

GeneView

GeneView via analysis of contig annotation: SYNPO2 synaptopodin 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_016354->NM_133477

function

HuRef

NW_001838920->NM_133477

function

Celera

NW_922195->NM_133477

function

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


reference	NT_016354->NM_133477->NP_597734	44441024	forward	intron

HuRef	NW_001838920->NM_133477->NP_597734	461679	forward	intron

Celera	NW_922195->NM_133477->NP_597734	422769	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6855192 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838920.1	461679	115615110	plus	T	alt_assembly_8	HuRef	HuRef	view	200
4	NW_922195.1	422769	117253431	plus	C	alt_assembly_1	Celera	Celera	view	200
4	NT_016354.18	44441024	120112327	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016354

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10182481	HapMap-CEU	European	108	IG	0.074	0.407	0.519	1.000	0.278	0.722

	HapMap-HCB	Asian	72	IG	0.167	0.556	0.278	0.479	0.444	0.556

	HapMap-JPT	Asian	72	IG		0.361	0.639	0.200	0.181	0.819

	HapMap-YRI	Sub-Saharan African	114	IG	0.193	0.456	0.351	0.655	0.421	0.579

ss23280577	AFD_EUR_PANEL	European	48	IG	0.042	0.500	0.458	0.317	0.292	0.708

	AFD_AFR_PANEL	African American	46	IG	0.261	0.348	0.391	0.200	0.435	0.565

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.292	0.667	1.000	0.188	0.812

ss68909400	HapMap-CEU	European	120	GF	0.067	0.400	0.533		0.267	0.733

	HapMap-HCB	Asian	90	GF	0.156	0.533	0.311		0.422	0.578

	HapMap-JPT	Asian	90	GF		0.333	0.667		0.167	0.833

	HapMap-YRI	Sub-Saharan African	120	GF	0.200	0.433	0.367		0.417	0.583

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss10182481	269	29	106	101
ss23280577	71	8	27	36
ss68909400	269	31	118	120

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs6855192	332	39	142	150

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5285	ss10182481	C/T	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	r23_ch4_YRI_perlegen:genotyping_1.0.0	2752090
5285	ss68909400	T/T	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	chr4-HapMap-YRI

Genotype data submitted for	341	samples from	332	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .