Reference SNP(refSNP) Cluster Report: rs3736238

Reference SNP(refSNP) Cluster Report: rs3736238

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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_004475.2:c.982G>A
NP_004466.2:p.Ala328Thr
NT_010799.14:g.1945319C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48411831 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3736238 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
ss4922236	YUSUKE\|IMS-JST080328	fwd/B	C/T	cctctgccttgcccatcgcctcgatgactg	cgcttccgcctccccgattttgcggatctt	07/24/02	10/10/03	107	Genomic	unknown
ss16245881	CGAP-GAI\|1489560	rev/T	A/G	aagatccgcaaaatcggggaggcggaagcg	cagtcatcgaggcgatgggcaaggcagagg	11/18/03	11/22/03	120	cDNA	unknown
ss24597263	PERLEGEN\|afd4229166	fwd/B	C/T	cctctgccttgcccatcgcctcgatgactg	cgcttccgcctccccgattttgcggatctt	08/10/04	08/21/04	123	Genomic	unknown
ss48411831	APPLERA_GI\|hCV25649134	fwd/B	C/T	cctctgccttgcccatcgcctcgatgactg	cgcttccgcctccccgattttgcggatctt	09/28/05	11/03/06	126	Genomic	unknown
ss69194077	PERLEGEN\|PGP04229166	fwd/B	C/T	cctctgccttgcccatcgcctcgatgactg	cgcttccgcctccccgattttgcggatctt	01/30/07	03/31/08	127	Genomic	unknown
ss74879758	ILLUMINA\|ILMN_Human_1M_rs3736238	fwd/B	C/T	cctctgccttgcccatcgcctcgatgactg	cgcttccgcctccccgattttgcggatctt	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 CTGTGGGCCA GGGATGGCTT AGGCCTTTGT AGGGTTCCTG CCCCCTGCTG AGGATGCTCC
 TCATTTAACC CTTCTAGCCA TCTGTCCCTG TGTTACTCGC AAGGCCCAGA GAAGTTCTGG
 CACTTGCCCA GCTTGTCAAG CAAGGACACT TGAACCCTAG GACCCGCTTG GGTGGAAGCC
 TCACCTGGGG CAGGGCCTCT AGCACCAAGG CCATCTTGGC TGCATCCCCG TATTTCTGGT
 AGGCTTCTGC CTTGAGCTTC ATCCGCTCAG CCTCTGCCTT GCCCATCGCC TCGATGACTG
 Y
 CGCTTCCGCC TCCCCGATTT TGCGGATCTT CTCAGCCTCT GCCTGTGCCA AGAGGACCTG
 CTTCACCCTG GGGGAGCCCA GGCCAGTTAG GATCAGTGGG ACGTACCAGG GTCCTCTCAA
 GCCTTGCCTG GGGGCCAGCA AACCTTCAAA CCCTCTGCTC TGGGGGCTGT CGGGGTGGGA
 GACATTGGAA CGGAGTGGGG TGGCCTGACC TTCCGGCTCT GGCCAGGGAA AGGCCACCGG
 CTCCCATCTG TAAGTGGGAG GGAACAAACC AGGATGCCGT CTATGCCCAA GCACTACACC

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
NC_000017.9 BU179554

dbSNP Blast Analysis

UniGene Cluster ID
514038

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss24597263	AFD_EUR_PANEL	European	48	IG	0.958	0.042	1.000	0.979	0.021

	AFD_AFR_PANEL	African American	46	IG	1.000			1.000

	AFD_CHN_PANEL	Asian	48	IG	1.000			1.000

ss48411831	HapMap-CEU	European	120	IG	0.967	0.033	1.000	0.983	0.017

	HapMap-HCB	Asian	90	IG	1.000			1.000

	HapMap-JPT	Asian	90	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	1.000			1.000

	AGI_ASP population	multiple	78	IG	0.974	0.026	1.000	0.987	0.013

ss4922236	JBIC-allele		1496	AF				0.967	0.034

ss69194077	HapMap-CEU	European	120	GF	0.983	0.017		0.992	0.008

	HapMap-HCB	Asian	90	GF	1.000			1.000

	HapMap-JPT	Asian	90	GF	1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.983	0.017		0.992	0.008

Concordant Genotype	Total Sample	C/C	C/T
ss24597263	71	70	1
ss48411831	987	934	26

RefSNP Genotype Summary	Total Individual	C/C	C/T
rs3736238	1046	993	27

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
255	ss48411831	C/T	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r27_ch17_CEU_illumina:human_1m_beadchip	5409397
361	ss48411831	C/T	CSHL-HAPMAP	HapMap-CEU	NA11993	CEPH1362.14	r27_ch17_CEU_illumina:human_1m_beadchip	5409397
5260	ss48411831	C/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r27_ch17_YRI_illumina:human_1m_beadchip	5409397

Genotype data submitted for	1061	samples from	1046	individuals	Individual with multiple genotypes submission:	15

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .