Reference SNP(refSNP) Cluster Report: rs195429

Reference SNP(refSNP) Cluster Report: rs195429

refSNP ID: rs195429
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/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_003958.3:c.1442-4083C>T
NM_183078.2:c.1237-4083C>T
NT_007592.14:g.28212685C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2751809 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs195429 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
ss257341	KWOK\|OVLP-000621-88521	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	06/30/00	10/10/03	79	Genomic	97 %
ss588388	SC_JCM\|AL096712.20_16033	rev/T	A/G	ggccagcaaccactgattttcactttcagt	caacatggtgcagggctcattggagtcact	07/12/00	04/07/04	80	Genomic	unknown
ss1033148	KWOK\|OVLP-000804-434621	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	09/02/00	10/10/03	86	Genomic	97 %
ss1838870	KWOK\|OVLP-000925-621005	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	10/05/00	10/10/03	87	Genomic	97 %
ss2751809	TSC-CSHL\|TSC0879824	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	01/02/01	04/07/04	92	Genomic	unknown
ss3202979	YUSUKE\|IMS-JST023063	rev/T	A/G	ggccagcaaccactgattttcactttcagt	caacatggtgcagggctcattggagtcact	09/05/01	10/10/03	100	Genomic	unknown
ss10326500	BCM_SSAHASNP\|chr6.NT_007592.13_28151562	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	06/29/03	10/10/03	116	Genomic	unknown
ss13085596	SC_SNP\|NT_007592.13_28151562	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	10/22/03	10/31/03	119	Genomic	unknown
ss17907534	CSHL-HAPMAP\|CSHL-HuCC-200402.chr6.NT_007592.13_28151562	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	02/19/04	03/04/04	120	Genomic	unknown
ss22473756	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007592.13_28151562	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	03/21/04	03/21/04	121	Genomic	unknown
ss23445237	PERLEGEN\|afd4059246	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	08/10/04	09/13/04	123	Genomic	unknown
ss44750356	ABI\|hCV2786831	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	07/19/05	11/03/06	126	Genomic	unknown
ss65785986	ILLUMINA\|Human1-rs195429	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	10/10/06	10/10/06	127	Genomic	unknown
ss66206754	AFFY\|SNP_A-2299355	fwd/B	C/T	gccctgcaccatgttg	actgaaagtgaaaatc	10/27/06	08/14/07	127	Genomic	unknown
ss66804670	ILLUMINA\|HumanHap300v1.1_rs195429	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	11/09/06	11/09/06	127	Genomic	unknown
ss67210254	ILLUMINA\|HumanHap550v1.1_rs195429	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	11/14/06	11/14/06	127	Genomic	unknown
ss67603288	ILLUMINA\|HumanHap650Yv1.0_rs195429	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	11/14/06	11/14/06	127	Genomic	unknown
ss68375190	CSHL-HAPMAP\|sanger:assay:383186:1	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	01/11/07	01/16/07	127	NA	unknown
ss70688510	ILLUMINA\|HumanHap550v3.0__rs195429	rev/T	A/G	ggccagcaaccactgattttcactttcagt	caacatggtgcagggctcattggagtcact	04/20/07	03/30/08	130	Genomic	unknown
ss71253157	ILLUMINA\|HumanHap650Yv3.0_rs195429	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	04/23/07	04/23/07	127	Genomic	unknown
ss75853065	ILLUMINA\|ILMN_Human_1M_rs195429	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	08/28/07	08/29/07	129	Genomic	unknown
ss76300425	AFFY\|AFFY_6_1M_SNP_A-2299355	fwd/B	C/T	gccctgcaccatgttg	actgaaagtgaaaatc	08/28/07	08/30/07	129	Genomic	unknown
ss79103726	ILLUMINA\|HumanHap300v2.0_rs195429	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	04/18/07	11/18/07	130	Genomic	unknown
ss83381998	KRIBB_YJKIM\|KHS448215	fwd/B	C/T	agtgactccaatgagccctgcaccatgttg	actgaaagtgaaaatcagtggttgctggcc	12/04/07	12/04/07	130	Genomic	unknown

Fasta sequence (Legend)

 ATGTATGGAA GATTGAGTTT GAGGGAACCA TGCATGCCAG AGTTGAGAGA TCCAGGGCTG
 ACTTTGACTG CTGGGCTACA ATAGCTTTAA ATACACCCTG AGGAGTCCAA TGCAGGAGAG
 TCAGTGACTC CAATGAGCCC TGCACCATGT TG
 Y
 ACTGAAAGTG AAAATCAGTG GTTGCTGGCC ATGGTGGGAT CCCATCGCTG CTGGAGGCTG
 CAGCCCAGCT ATCAGCCCAC CAGCCTAGCT TGTCCATCAG GCTGGGAAAA GGGCCTGGAG
 ATGGAACATG AGCAGTTCTG GCCATCTCTG GTGTTTAGCA GGAGACACTT CAGATTGTTC
 ATTGCTATTT CCCACAGTAA AATTTTCTCC TGCCCTTTTT TGATTTTTAG TGATAACACA
 GTTATTTTGG CCCTCTAAAA AATGGATCCT CTTTCCCTCC TAACGTGTAA TTTTATCATT
 TTTCATACCT ACTTCCAGGA ATGTCTATTG TAGGAGACTA CCTGTGCAAA TATAGAGTAG
 CGTCATTAAC CAAAGCAGCT TTTCTTTGAG TTTCTTGGTT AACCCTAGAT GAACACTGAG
 TATTTTTAGA GCAAGCTCAA ATAAGTTGAT ATTCTATGAA CTAATCATAG AGAATGGCTG
 ATTATACCT

GeneView

GeneView via analysis of contig annotation: RNF8 ring finger protein 8

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_007592->NM_003958

function

reference

NT_007592->NM_183078

function

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


reference	NT_007592->NM_003958->NP_003949	28212685	forward	intron

reference	NT_007592->NM_183078->NP_898901	28212685	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs195429 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838980.1	10345565	37073256	plus	T	alt_assembly_8	HuRef	HuRef	view	152
6	NT_007592.14	28212685	37462413	plus	C	ref_assembly	reference	reference	view	152
6	NW_923073.1	10373729	38909408	plus	T	alt_assembly_1	Celera	Celera	view	152

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592 AC026004 AL096712.20

dbSNP Blast Analysis
GenBank HTGS Finished:
AL096712.20

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23445237	AFD_EUR_PANEL	European	48	IG	0.833	0.167		0.752	0.917	0.083

	AFD_AFR_PANEL	African American	46	IG	0.130	0.478	0.391	1.000	0.370	0.630

	AFD_CHN_PANEL	Asian	48	IG	0.875	0.125		0.752	0.938	0.062

ss2751809	CEPH		184	AF					0.900	0.100

	HapMap-CEU	European	120	IG	0.833	0.167		0.527	0.917	0.083

	HapMap-HCB	Asian	90	IG	0.711	0.289		0.273	0.856	0.144

	HapMap-JPT	Asian	88	IG	0.636	0.341	0.023	0.584	0.807	0.193

	HapMap-YRI	Sub-Saharan African	120	IG	0.067	0.433	0.500	0.655	0.283	0.717

ss3202979	JBIC-allele		1312	AF					0.851	0.149

ss44750356	AoD_African_American		90	AF					0.390	0.610

	AoD_Caucasian		92	AF					0.920	0.080

	AoD_Chinese		90	AF					0.890	0.110

	AoD_Japanese		90	AF					0.850	0.150

ss588388	SC_12_A	Asian	24	IG	0.917	0.083		1.000	0.958	0.042

	SC_12_AA	African American	24	IG	0.167	0.333	0.500	0.403	0.333	0.667

	SC_12_C	European	14	IG	0.857	0.143		1.000	0.929	0.071

	SC_95_C	European	94	IG	0.809	0.191		0.479	0.904	0.096

ss66206754	HapMap-CEU	European	118	GF	0.831	0.169			0.915	0.085

	HapMap-HCB	Asian	90	GF	0.711	0.289			0.856	0.144

	HapMap-JPT	Asian	90	GF	0.644	0.333	0.022		0.811	0.189

	HapMap-YRI	Sub-Saharan African	120	GF	0.067	0.433	0.500		0.283	0.717

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss23445237	71	44	18	9
ss2751809	269	137	84	46
ss588388	123
ss66206754	268	138	84	46

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs195429	401	175	101	55

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
229	ss588388	A/G	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229	ss588388	G/G	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss2751809	C/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch6_CEU_illumina:golden_gate_1.0.0
229	ss66206754	C/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr6-HapMap-CEU
230	ss588388	A/G	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
230	ss588388	G/G	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE

Genotype data submitted for	472	samples from	401	individuals	Individual with multiple genotypes submission:	285

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 .