Reference SNP(refSNP) Cluster Report: rs3752087

Reference SNP(refSNP) Cluster Report: rs3752087

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/130
Map to Genome Build:	36.3
Citation:	PubMed

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_002747.3:c.112G>A
NP_002738.2:p.Val38Met
NT_010966.13:g.29679542G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76900192 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3752087 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
ss4938115	YUSUKE\|IMS-JST104196	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	08/01/02	10/10/03	107	Genomic	unknown
ss17602982	CSHL-HAPMAP\|CSHL-HuCC-200402.chr18.NT_010966.13_29679542	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	02/19/04	03/04/04	120	Genomic	unknown
ss21442303	SSAHASNP\|WGSA-200403-chr18.chr18.NT_010966.13_29679542	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	03/20/04	03/20/04	121	Genomic	unknown
ss40952926	ABI\|hCV3226313	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	07/17/05	11/03/06	126	Genomic	unknown
ss48533640	CANCER-GENOME\|NC_000018.8_46444438	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	10/20/05	11/29/05	126	Genomic	unknown
ss65731446	ILLUMINA\|Human1-rs3752087	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	10/10/06	10/10/06	127	Genomic	unknown
ss66778936	ILLUMINA\|HumanHap300v1.1_rs3752087	fwd/B	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	11/09/06	11/09/06	127	Genomic	unknown
ss67299651	ILLUMINA\|HumanHap550v1.1_rs3752087	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	11/14/06	11/14/06	127	Genomic	unknown
ss67704312	ILLUMINA\|HumanHap650Yv1.0_rs3752087	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	11/14/06	11/14/06	127	Genomic	unknown
ss68409608	CSHL-HAPMAP\|sanger:assay:4250390:1	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	01/11/07	01/16/07	127	NA	unknown
ss69214513	PERLEGEN\|PGP04230178	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	01/30/07	03/31/08	127	Genomic	unknown
ss70778280	ILLUMINA\|HumanHap550v3.0__rs3752087	rev/B	C/T	cagcgaccttccggcaggcccggctgtcca	ggccgacagcaccaaaccattgacaccgaa	04/20/07	03/30/08	130	Genomic	unknown
ss71354480	ILLUMINA\|HumanHap650Yv3.0_rs3752087	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	04/23/07	04/23/07	127	Genomic	unknown
ss75796697	ILLUMINA\|ILMN_Human_1M_rs3752087	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	08/28/07	08/29/07	129	Genomic	unknown
ss76900192	SI_EXO\|NT_010966.13_29679542	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	09/20/07	09/20/07	129	Genomic	unknown
ss78180686	HGSV\|Cor12878_SNV_20070510.chr18_46444438	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	10/17/07	10/18/07	129	Genomic	unknown
ss79164862	ILLUMINA\|HumanHap300v2.0_rs3752087	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	04/18/07	11/18/07	130	Genomic	unknown
ss82504733	HGSV\|Cor18956_SNV_20070510.chr18_46444438	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	11/30/07	12/03/07	130	Genomic	unknown
ss84169226	KRIBB_YJKIM\|KHS649466	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	12/04/07	12/06/07	130	Genomic	unknown
ss86270807	CORNELL\|hCV3226313	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	01/21/08	01/21/08	129	Genomic	unknown
ss90792026	BCMHGSC_JDW\|JWB-1099945	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	02/26/08	03/01/08	129	Genomic	unknown
ss110529541	1000GENOMES\|CEU.trio.12.15.2008_3513950_chr18_46444438	fwd/T	A/G	ttcggtgtcaatggtttggtgctgtcggcc	tggacagccgggcctgccggaaggtcgctg	12/15/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 CCATTCTAAG CTTTAAGAAG GGTTCAGGAA ACACAGGAAT TAGTAGACAG CCCTCCCAAT
 GCAGGTTAAG ACGACAGCCT GCGCCCCCAA CTAGCACAGC TCAGCGAGCA TGACCATATG
 CCATTCTCGT CTCCAGAGAG CTGGTGGCAG TGACCTCACT AGGAGAAAAC ACATCCCTCA
 GCCGTGGGAC TTGACAGAAT GAGGTGCGCG AGGGAGGCCG CTAGCCGAGA CTTGGCCTTT
 CCTGACTGCC CCTGTGTTAC CTGGGCAGCT CCAGATCACT GAGCCCACAA TGGCTGAGAA
 GGGTGACTGC ATCGCCAGTG TCTATGGGTA TGACCTCGGT GGGCGCTTTG TTGACTTCCA
 ACCCCTGGGC TTCGGTGTCA ATGGTTTGGT GCTGTCGGCC
 R
 TGGACAGCCG GGCCTGCCGG AAGGTCGCTG TGAAGAAGAT TGCCCTGAGC GATGCCCGCA
 GCATGAAGCA CGCGCTCCGA GAGATCAAGA TCATTCGGCG CCTGGACCAC GACAACATCG
 TCAAAGTGTA CGAGGTGCTC GGTCCCAAGG GCACTGACCT GCAGGGTGAG CTGTTCAAGT
 TCAGCGTGGC GTACATCGTC CAGGAGTACA TGGAGACCGA CCTGGCACGC CTGCTGGAGC
 AGGGCACGCT GGCAGAAGAG CATGCCAAGC TGTTCATGTA CCAGCTGCTC CGCGGGCTCA
 AGTACATCCA CTCCGCCAAC GTGCTGCACA GGGACCTGAA GCCCGCCAAC ATCTTCATCA
 GCACAGAGGA CCTCGTGCTC AAGATTGGGG ATTTCGGGTT

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_025007.1

dbSNP Blast Analysis

UniGene Cluster ID
433728

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss40952926	HapMap-CEU	European	120	IG	0.183	0.550	0.267	0.439	0.458	0.542

	HapMap-HCB	Asian	90	IG	0.133	0.600	0.267	0.100	0.433	0.567

	HapMap-JPT	Asian	86	IG	0.209	0.488	0.302	1.000	0.453	0.547

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.183	0.783	0.251	0.125	0.875

ss4938115	JBIC-allele		748	AF					0.444	0.556

ss69214513	HapMap-CEU	European	120	GF	0.200	0.500	0.300		0.450	0.550

	HapMap-HCB	Asian	90	GF	0.133	0.556	0.311		0.411	0.589

	HapMap-JPT	Asian	90	GF	0.222	0.489	0.289		0.467	0.533

	HapMap-YRI	Sub-Saharan African	120	GF	0.033	0.200	0.767		0.133	0.867

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss76900192	1197	115	435	626

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs3752087	1207	115	435	626

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
151	ss76900192	A/A	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r27_ch18_CEU_illumina:human_1m_beadchip
174	ss76900192	N/N	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	r27_ch18_CEU_illumina:human_1m_beadchip
184	ss76900192	N/N	CSHL-HAPMAP	HapMap-CEU	NA07034	CEPH1341.11	r27_ch18_CEU_illumina:human_1m_beadchip
186	ss76900192	A/A	CSHL-HAPMAP	HapMap-CEU	NA06993	CEPH1341.13	r27_ch18_CEU_illumina:human_1m_beadchip
200	ss76900192	A/G	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r27_ch18_CEU_illumina:human_1m_beadchip
226	ss76900192	G/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch18_CEU_illumina:human_1m_beadchip
548	ss76900192	A/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch18_CEU_illumina:human_1m_beadchip
5141	ss76900192	G/G	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	r27_ch18_YRI_illumina:human_1m_beadchip
5161	ss76900192	A/G	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r27_ch18_CHB_illumina:human_1m_beadchip
5186	ss76900192	A/G	CSHL-HAPMAP	HapMap-HCB	NA18582	CH18582	r27_ch18_CHB_illumina:human_1m_beadchip

Genotype data submitted for	1207	samples from	1207	individuals	Individual with multiple genotypes submission:	0

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 .