Reference SNP(refSNP) Cluster Report: rs2246945

Reference SNP(refSNP) Cluster Report: rs2246945

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/130
Map to Genome Build:	36.3

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

HGVS Names
NM_016161.1:c.653C>A
NM_016161.2:c.653C>A
NP_057245.1:p.Ala218Asp
NT_005612.15:g.44338622G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss105438128 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2246945 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
ss3233391	YUSUKE\|IMS-JST043476	fwd/T	A/C	tggaaaactttgttgaacactataattcag	catttggggcaaccaaggccctgagttgat	09/05/01	10/10/03	100	Genomic	unknown
ss3692921	SC_JCM\|AC022738.3_104117	fwd/T	A/C	tggaaaactttgttgaacactataattcag	catttggggcaaccaaggccctgagttgat	09/24/01	10/25/06	100	Genomic	unknown
ss11588969	WI_SSAHASNP\|chr3.NT_005612.13_44243012	rev/B	G/T	atcaactcagggccttggttgccccaaatg	ctgaattatagtgttcaacaaagttttcca	07/03/03	10/10/03	116	Genomic	unknown
ss14242234	BCM_SSAHASNP\|chr3.NT_005612.14_44338630	rev/B	G/T	atcaactcagggccttggttgccccaaatg	ctgaattatagtgttcaacaaagttttcca	11/05/03	11/22/03	119	Genomic	unknown
ss68876610	PERLEGEN\|PGP04748844	rev/B	G/T	atcaactcagggccttggttgccccaaatg	ctgaattatagtgttcaacaaagttttcca	01/30/07	08/14/07	127	Genomic	unknown
ss74867193	ILLUMINA\|ILMN_Human_1M_rs2246945	fwd/T	A/C	tggaaaactttgttgaacactataattcag	catttggggcaaccaaggccctgagttgat	08/28/07	08/29/07	129	Genomic	unknown
ss86239916	CORNELL\|hCV16041755	rev/T	A/C	atcaactcagggccttggttgccccaaatg	ctgaattatagtgttcaacaaagttttcca	01/21/08	01/21/08	129	Genomic	unknown
ss105438128	SNP500CANCER\|A4GNT-01	fwd/T	A/C	tggaaaactttgttgaacactataattcag	catttggggcaaccaaggccctgagttgat	09/05/08	09/05/08	130	Genomic	unknown
ss112506256	1000GENOMES\|CEU.trio.12.15.2008_815167_chr3_139326166	rev/B	G/T	atcaactcagggccttggttgccccaaatg	ctgaattatagtgttcaacaaagttttcca	12/15/08	12/17/08	130	Genomic	unknown
ss117290155	ILLUMINA-UK\|NA18507_000177844_NCBI36.1_chr3_139326166	rev/B	G/T	atcaactcagggccttggttgccccaaatg	ctgaattatagtgttcaacaaagttttcca	01/18/09	01/19/09	130	Genomic	99 %

Fasta sequence (Legend)

 GATGCCCCTC CCTCTTCCCC TGGCTACTTG GGGCTGATTT GCACCTGCTC CTGCAGATCA
 ACGCCAGCGC AGAGAGAAAC TGGCTCCACA TCAGCTCGGA TGCATCCCGC CTGGCCATCA
 TCTGGAAATA CGGTGGCATC TACATGGACA CCGATGTCAT CTCCATCAGG CCCATCCCTG
 AGGAGAACTT TTTGGCTGCG CAGGCTTCTC GGTACTCTAG TAATGGAATA TTTGGGTTCC
 TCCCCCACCA CCCCTTTTTG TGGGAATGCA TGGAAAACTT TGTTGAACAC TATAATTCAG
 M
 CATTTGGGGC AACCAAGGCC CTGAGTTGAT GACAAGGATG TTGAGGGTAT GGTGTAAACT
 TGAAGACTTC CAGGAGGTGA GCGACCTCAG GTGTCTGAAC ATATCCTTCT TACACCCCCA
 AAGATTTTAC CCCATCTCCT ATCGAGAGTG GAGGCGCTAC TATGAAGTGT GGGATACAGA
 GCCAAGCTTC AATGTCTCTT ATGCCCTGCA TTTGTGGAAC CACATGAACC AGGAGGGGCG
 GGCTGTGATT AGAGGAAGCA ACACACTGGT GGAAAATCTC TATCGCAAGC ACTGTCCCAG

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_005612 AC084436

dbSNP Blast Analysis

UniGene Cluster ID
278960

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss105438128	P1		196	GF	0.469	0.378	0.153		0.658	0.342

	CAUC1		58	GF	0.586	0.310	0.103		0.741	0.259

	AFR1		48	GF	0.458	0.333	0.208		0.625	0.375

	HISP1		44	GF	0.364	0.500	0.136		0.614	0.386

	PAC1		46	GF	0.435	0.391	0.174		0.630	0.370

	P2		418	GF	0.455	0.450	0.096		0.679	0.321

	CAUC2		118	GF	0.525	0.407	0.068		0.729	0.271

	AFR2		120	GF	0.400	0.467	0.133		0.633	0.367

	ASI2		180	GF	0.444	0.467	0.089		0.678	0.322

ss3233391	JBIC-allele		1484	AF					0.588	0.412

ss3692921	HapMap-CEU	European	120	IG	0.533	0.400	0.067	1.000	0.733	0.267

	HapMap-HCB	Asian	84	IG	0.595	0.381	0.024	0.403	0.786	0.214

	HapMap-JPT	Asian	86	IG	0.302	0.535	0.163	0.584	0.570	0.430

	HapMap-YRI	Sub-Saharan African	120	IG	0.400	0.467	0.133	1.000	0.633	0.367

ss68876610	HapMap-CEU	European	120	GF	0.533	0.400	0.067		0.733	0.267

	HapMap-HCB	Asian	90	GF	0.578	0.400	0.022		0.778	0.222

	HapMap-JPT	Asian	90	GF	0.311	0.533	0.156		0.578	0.422

	HapMap-YRI	Sub-Saharan African	120	GF	0.400	0.467	0.133		0.633	0.367

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.438+/-0.165	1207	1002	270	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .