Reference SNP(refSNP) Cluster Report: rs795992

Reference SNP(refSNP) Cluster Report: rs795992

refSNP ID: rs795992
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_018717.3:c.2079+74289C>T
NT_016354.18:g.65284369G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2272789 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs795992 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
ss988267	KWOK\|OVLP-000804-625400	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	09/01/00	10/10/03	86	Genomic	99 %
ss1623131	KWOK\|OVLP-000925-580260	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	10/04/00	10/10/03	87	Genomic	99 %
ss2272789	TSC-CSHL\|TSC0686776	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	10/20/00	05/17/04	88	Genomic	95 %
ss3763303	SC_JCM\|AC044906.2_165674	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	09/25/01	10/10/03	100	Genomic	unknown
ss10106335	BCM_SSAHASNP\|chr4.NT_016606.15_2255887	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	06/27/03	10/10/03	116	Genomic	unknown
ss11616947	WI_SSAHASNP\|chr4.NT_016606.15_2255887	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	07/03/03	10/10/03	116	Genomic	unknown
ss17032488	CSHL-HAPMAP\|CSHL-HuAA-200402.chr4.NT_016606.16_2284278	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	02/17/04	03/04/04	120	Genomic	unknown
ss17811164	CSHL-HAPMAP\|CSHL-HuCC-200402.chr4.NT_016606.16_2284278	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	02/19/04	03/04/04	120	Genomic	unknown
ss22118658	SSAHASNP\|WGSA-200403-chr4.chr4.NT_016606.16_2284278	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	03/20/04	03/21/04	121	Genomic	unknown
ss46542955	PERLEGEN\|PS02778288	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	08/01/05	08/01/05	126	Genomic	unknown
ss66091792	AFFY\|SNP_A-1948005	fwd/T	A/G	tttagaccacatgaga	ccaaaacctaattttg	10/27/06	08/14/07	127	Genomic	unknown
ss66660651	ILLUMINA\|HumanHap300v1.1_rs795992	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	11/09/06	11/09/06	127	Genomic	unknown
ss67853022	ILLUMINA\|HumanHap550v1.1_rs795992	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	11/14/06	11/14/06	127	Genomic	unknown
ss68005014	ILLUMINA\|HumanHap650Yv1.0_rs795992	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	11/14/06	11/15/06	127	Genomic	unknown
ss68913031	PERLEGEN\|PGP02778288	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	01/30/07	08/14/07	127	Genomic	unknown
ss70961068	ILLUMINA\|HumanHap550v3.0__rs795992	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	04/20/07	03/31/08	130	Genomic	unknown
ss71569588	ILLUMINA\|HumanHap650Yv3.0_rs795992	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	04/23/07	04/23/07	127	Genomic	unknown
ss75517233	ILLUMINA\|ILMN_Human_1M_rs795992	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	08/28/07	08/29/07	129	Genomic	unknown
ss76046638	AFFY\|AFFY_6_1M_SNP_A-1948005	fwd/T	A/G	tttagaccacatgaga	ccaaaacctaattttg	08/28/07	08/29/07	129	Genomic	unknown
ss77582294	HGSV\|Cor12156_SNV_20070510.chr4_141093827	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	10/09/07	10/13/07	129	Genomic	unknown
ss79049726	HGSV\|Cor18507_SNV_20070510.chr4_141093827	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	10/19/07	10/22/07	129	Genomic	unknown
ss79276212	ILLUMINA\|HumanHap300v2.0_rs795992	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	04/18/07	11/18/07	130	Genomic	unknown
ss80750929	KRIBB_YJKIM\|KHS1001870	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	11/26/07	11/26/07	130	Genomic	unknown
ss83565818	KRIBB_YJKIM\|KHS491186	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	12/04/07	12/05/07	130	Genomic	unknown
ss83653083	HGSV\|Cor18956_SNV_20070510.chr4_141093827	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	11/30/07	12/05/07	130	Genomic	unknown
ss92802854	BCMHGSC_JDW\|JWB-1862422	fwd/T	A/G	tgagtgtacttggatttagaccacatgaga	ccaaaacctaattttgatgagaaactaaaa	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTTCCTTCCC ACACCCAGTA AAGAGCGTAG GGCTGGAGGA ACCTGGGCAA CGGAAGACAA
 AGGGAATTTT CTACAGAGAG TTTTATATGC TATTTCCATG GCTGTGCTAT AGAAATGAAA
 GAGTATCATT AGGGTTTAGA GTCTAATGAG GCAGCATTAG ATAGGCCAAG GAAAAGTCAC
 TCTATGTAAA ATATAATTAT CTGGAGAAGA AAAGTGAGTG TACTTGGATT TAGACCACAT
 GAGA
 R
 CCAAAACCTA ATTTTGATGA GAAACTAAAA TTCTGGCTAT GCAAAAGGCA GACTAGGAAG
 CTAGAAAGCC CGACTTATGA ATAAAAGACA AATAGGTCTG TTCTGGAACT TGGTGTCCAC
 TTAGTATCCA TAACATGGAT GGTTTGTAAA TTCAGGAATA AGGGAAGGTA AGATCCTGAA
 GTGTACTGTG CTTGCTAAAA GAAACTGTTT TCAGGAATGA ATCATTTCTC TTACAACAGG
 TAAATATGGC CTGCTGAATA ATAATAGCCC ACATTCATTC AGAGCTTATT ATGTGCTAGG
 CACTTTAAAG TGCTTTATAA ATACTAGCTT ATTT

GeneView

GeneView via analysis of contig annotation: MAML3 mastermind-like 3 (Drosophila)

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_018717

function

HuRef

NW_001838921->NM_018717

function

Celera

NW_922217->NM_018717

function

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


reference	NT_016354->NM_018717->NP_061187	65284369	reverse	intron

HuRef	NW_001838921->NM_018717->NP_061187	947604	reverse	intron

Celera	NW_922217->NM_018717->NP_061187	20326122	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs795992 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_001838921.1	947604	136465365	plus	A	alt_assembly_8	HuRef	HuRef	view	244
4	NW_922217.1	20326122	138068643	plus	A	alt_assembly_1	Celera	Celera	view	244
4	NT_016354.18	65284369	140955672	plus	G	ref_assembly	reference	reference	view	244

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016606 AC019343 AC044906.2

dbSNP Blast Analysis
GenBank HTGS Finished:
AC097464.3 NC_000004.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss2272789	HapMap-CEU	European	120	IG	0.567	0.383	0.050	0.752	0.758	0.242

	HapMap-HCB	Asian	90	IG	0.756	0.222	0.022	1.000	0.867	0.133

	HapMap-JPT	Asian	88	IG	0.591	0.409		0.100	0.795	0.205

	HapMap-YRI	Sub-Saharan African	120	IG	0.633	0.333	0.033	0.752	0.800	0.200

ss66091792	HapMap-CEU	European	118	GF	0.559	0.390	0.051		0.754	0.246

	HapMap-HCB	Asian	90	GF	0.756	0.222	0.022		0.867	0.133

	HapMap-JPT	Asian	90	GF	0.556	0.444			0.778	0.222

	HapMap-YRI	Sub-Saharan African	120	GF	0.633	0.333	0.033		0.800	0.200

ss68913031	HapMap-CEU	European	120	GF	0.567	0.383	0.050		0.758	0.242

	HapMap-HCB	Asian	90	GF	0.756	0.222	0.022		0.867	0.133

	HapMap-JPT	Asian	90	GF	0.578	0.422			0.789	0.211

	HapMap-YRI	Sub-Saharan African	120	GF	0.633	0.333	0.033		0.800	0.200

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss2272789	269	167	90	11
ss66091792	268	166	91	11
ss68913031	269	167	91	11

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs795992	270	167	91	11

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5229	ss2272789	A/A	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	r23_ch4_JPT_illumina:golden_gate_1.0.0	477369
5229	ss66091792	A/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr4-HapMap-JPT
5229	ss68913031	A/A	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr4-HapMap-JPT

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

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .