Reference SNP(refSNP) Cluster Report: rs3784246

Reference SNP(refSNP) Cluster Report: rs3784246

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

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

HGVS Names
NM_018958.2:c.635T>C
NP_061831.2:p.Val212Ala
NT_026446.13:g.1356448T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48409423 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3784246 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
ss4970601	YUSUKE\|IMS-JST140695	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	08/12/02	10/10/03	107	Genomic	unknown
ss48409423	APPLERA_GI\|hCV22274534	rev/B	C/T	gatgcagccctgggcctctggagggaaatg	ctaccacaagttctcagaaaacagcatgag	09/28/05	11/03/06	126	Genomic	unknown
ss65727884	ILLUMINA\|Human1-rs3784246	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	10/10/06	10/10/06	127	Genomic	unknown
ss66840502	ILLUMINA\|HumanHap300v1.1_rs3784246	fwd/B	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	11/09/06	11/09/06	127	Genomic	unknown
ss67302817	ILLUMINA\|HumanHap550v1.1_rs3784246	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	11/14/06	11/14/06	127	Genomic	unknown
ss67707746	ILLUMINA\|HumanHap650Yv1.0_rs3784246	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	11/14/06	11/14/06	127	Genomic	unknown
ss69170388	PERLEGEN\|PGP04397149	rev/B	C/T	gatgcagccctgggcctctggagggaaatg	ctaccacaagttctcagaaaacagcatgag	01/30/07	03/31/08	127	Genomic	unknown
ss70781468	ILLUMINA\|HumanHap550v3.0__rs3784246	rev/B	C/T	gatgcagccctgggcctctggagggaaatg	ctaccacaagttctcagaaaacagcatgag	04/20/07	03/30/08	130	Genomic	unknown
ss71357935	ILLUMINA\|HumanHap650Yv3.0_rs3784246	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	04/23/07	04/23/07	127	Genomic	unknown
ss75897785	ILLUMINA\|ILMN_Human_1M_rs3784246	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	08/28/07	08/29/07	129	Genomic	unknown
ss79167078	ILLUMINA\|HumanHap300v2.0_rs3784246	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	04/18/07	11/18/07	130	Genomic	unknown
ss84182845	KRIBB_YJKIM\|KHS652463	fwd/T	A/G	ctcatgctgttttctgagaacttgtggtag	catttccctccagaggcccagggctgcatc	12/04/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 GGAGGAATAC AGAAAGGCTT CTCATCAGGC ATCCTCTTTC CGGACATCAG CGGAATCGGC
 AAGCCTAGGG AGCTGGGCGG TGGCTCTTCA TTCAGCACTT CCGCAGCCAA CTTCTGCTGC
 AGCAGGGAGC AGCCAACGGC TGGCTCAGGG GGCGCTGTTG CATCCGGATC AGGCTTTCCA
 AGATGCCGGG CACATCCGGC CTGGCTGTGT GTGCTGGGCA TGGCAGGGCC TTCCAAGCAG
 GAGCTCGCTG GAGACGCCTG GGCCTTCTCA CTCATGCTGT TTTCTGAGAA CTTGTGGTAG
 R
 CATTTCCCTC CAGAGGCCCA GGGCTGCATC TGAAGGAGGC CACGTCTCCC TGGGTGCCCT
 GGGACCTGGA TGTGGACGAT GCTTCTCCGC TGCTAAGGGG GGTCCTTTTC TCGTCATCCT
 CCCCTTCGAT CTGCACCGGA TCCTCATCCT TCTTCACTCT TCTGGGCCCT TCTTGGGCCC
 ACACCTCGGT CTCCTCCAGG AGAGTGGCTG GGATGGGCTT CCTGGCCTTG ACCGCCGGCT
 CACGTGGTGA AGGCAGCAGG AGAGTGAACA TGCGGCTGGG AGGAGGGATC CTTACGGAAC

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_010178.1

dbSNP Blast Analysis

UniGene Cluster ID
451286

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss48409423	HapMap-CEU	European	120	IG	0.833	0.167		0.527	0.917	0.083

	HapMap-HCB	Asian	90	IG	0.622	0.356	0.022	0.479	0.800	0.200

	HapMap-JPT	Asian	88	IG	0.818	0.182		0.527	0.909	0.091

	HapMap-YRI	Sub-Saharan African	120	IG	0.950	0.050		1.000	0.975	0.025

	AGI_ASP population	multiple	52	IG	0.846	0.115	0.038	0.100	0.904	0.096

ss4970601	JBIC-allele		1478	AF					0.882	0.118

ss69170388	HapMap-CEU	European	120	GF	0.767	0.233			0.883	0.117

	HapMap-HCB	Asian	90	GF	0.622	0.378			0.811	0.189

	HapMap-JPT	Asian	90	GF	0.800	0.200			0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	GF	0.917	0.083			0.958	0.042

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss48409423	1230
ss69170388	261

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs3784246	1239

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
161	ss48409423	T/T	CSHL-HAPMAP	HapMap-CEU	NA07029	CEPH1340.01	r27_ch15_CEU_illumina:human_1m_beadchip	841664
161	ss69170388	C/T	CSHL-HAPMAP	HapMap-CEU	NA07029	CEPH1340.01	chr15-HapMap-CEU
170	ss48409423	T/T	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	r27_ch15_CEU_illumina:human_1m_beadchip	841664
170	ss69170388	C/T	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	chr15-HapMap-CEU
225	ss48409423	T/T	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch15_CEU_illumina:human_1m_beadchip	841664
225	ss69170388	C/T	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	chr15-HapMap-CEU
619	ss48409423	T/T	CSHL-HAPMAP	HapMap-CEU	NA12873	CEPH1459.10	r27_ch15_CEU_illumina:human_1m_beadchip	841664
619	ss69170388	C/T	CSHL-HAPMAP	HapMap-CEU	NA12873	CEPH1459.10	chr15-HapMap-CEU
636	ss48409423	T/T	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	r27_ch15_CEU_illumina:human_1m_beadchip	841664
636	ss69170388	C/T	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	chr15-HapMap-CEU
5177	ss48409423	C/C	CSHL-HAPMAP	HapMap-HCB	NA18594	CH18594	r27_ch15_CHB_illumina:human_1m_beadchip	841664
5177	ss69170388	C/T	CSHL-HAPMAP	HapMap-HCB	NA18594	CH18594	chr15-HapMap-HCB
5222	ss48409423	T/T	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r27_ch15_JPT_illumina:human_1m_beadchip	841664
5222	ss69170388	C/T	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	chr15-HapMap-JPT
5257	ss48409423	T/T	CSHL-HAPMAP	HapMap-YRI	NA18852	YOR018.02	r27_ch15_YRI_illumina:human_1m_beadchip	841664
5257	ss69170388	C/T	CSHL-HAPMAP	HapMap-YRI	NA18852	YOR018.02	chr15-HapMap-YRI
5285	ss48409423	T/T	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	r27_ch15_YRI_illumina:human_1m_beadchip	841664
5285	ss69170388	C/T	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	chr15-HapMap-YRI

Genotype data submitted for	1239	samples from	1239	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
	UNKNOWN	UNKNOWN	UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .