Reference SNP(refSNP) Cluster Report: rs1043657

Reference SNP(refSNP) Cluster Report: rs1043657

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
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_003689.2:c.424G>A
NP_003680.2:p.Ala142Thr
NT_004610.18:g.2459353C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48403433 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1043657 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
ss1511987	LEE\|80515	fwd/T	A/G	tgtccccaagtggacctcttctacctacac	cacctgaccacggcaccccggtggaagaga	09/13/00	10/10/03	86	cDNA	unknown
ss9837570	BCM_SSAHASNP\|chr1.NT_004610.15_438261	rev/B	C/T	tctcttccaccggggtgccgtggtcaggtg	gtgtaggtagaagaggtccacttggggaca	06/27/03	10/10/03	116	Genomic	unknown
ss24796060	SEQUENOM\|sqnm137522	fwd/T	A/G	tgtccccaagtggacctcttctacctacac	cacctgaccacggcaccccggtggaagaga	06/18/04	06/18/04	123	cDNA	unknown
ss48403433	APPLERA_GI\|hCV8860122	rev/B	C/T	tctcttccaccggggtgccgtggtcaggtg	gtgtaggtagaagaggtccacttggggaca	09/28/05	11/03/06	126	Genomic	unknown
ss68760431	PERLEGEN\|PGP03978529	rev/B	C/T	tctcttccaccggggtgccgtggtcaggtg	gtgtaggtagaagaggtccacttggggaca	01/30/07	08/14/07	127	Genomic	unknown
ss74856891	ILLUMINA\|ILMN_Human_1M_rs1043657	fwd/T	A/G	tgtccccaagtggacctcttctacctacac	cacctgaccacggcaccccggtggaagaga	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 ACATATATGA CATTATTTAA TCCCCAGGAC CTCCCAATGA GGACAGTTTG ATTATTATCA
 CCCCATTTTA CAGATCATAC AATTGAGGCC AAGAGAATAT TAGTAATTTA GCCAGGGTTA
 CATGGTTAGC AAATGGCTCT AATAGGTCAC TTAACCATTC CATTCTCTCT CCAAGTGAAA
 ATTGCCACCA AGGCCAACCC TTGGGATGGA AAATCACTAA AGCCTGACAG TGTCCGGTCC
 CAGCTGGAGA CGTCATTGAA GAGGCTGCAG TGTCCCCAAG TGGACCTCTT CTACCTACAC
 R
 CACCTGACCA CGGCACCCCG GTGGAAGAGA CGCTGCATGC CTGCCAGCGG CTGCACCAGG
 AGGTGAGGGG GCCCTCCGAG CTCCAAAGGT GGGCTCCTGC TCCTTTCTTT ATCCTGATCC
 TACTCATGAG AGCAGAGGCA CCAGGGCAGT CCCAGGGTGG GGCAGGGAAT AGCCCCATTC
 CCTGGGGCCC CACCCTGGCC TCCCCTTCCT GGTCTGGGCT ACACTGCGTT CTGACTGGAG
 CCTCACCCAT GCAGGGCAAG TTCGTGGAGC TTGGCCTCTC CAACTATGCT AGCTGGGAAG

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
dbSTS	GenBank
sqnm137522	NT_004610 Hs.6980

dbSNP Blast Analysis

UniGene Cluster ID
512807

3D structure mapping
NP_003680

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss48403433	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	88	IG		1.000			1.000

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

	AGI_ASP population	multiple	42	IG	0.238	0.762	0.584	0.119	0.881

ss68760431	HapMap-CEU	European	120	GF	0.100	0.900		0.050	0.950

	HapMap-HCB	Asian	90	GF	0.022	0.978		0.011	0.989

	HapMap-JPT	Asian	90	GF		1.000			1.000

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

Concordant Genotype	Total Sample	A/G	G/G
ss48403433	1042

RefSNP Genotype Summary	Total Individual	A/G	G/G
rs1043657	1055

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
172	ss48403433	T/T	CSHL-HAPMAP	HapMap-CEU	NA07056	CEPH1340.12	r27_ch1_CEU_illumina:human_1m_beadchip
225	ss48403433	C/T	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch1_CEU_illumina:human_1m_beadchip
226	ss48403433	C/C	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch1_CEU_illumina:human_1m_beadchip
229	ss48403433	C/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r27_ch1_CEU_illumina:human_1m_beadchip
239	ss48403433	C/T	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	r27_ch1_CEU_illumina:human_1m_beadchip
524	ss48403433	C/T	CSHL-HAPMAP	HapMap-CEU	NA12740	CEPH1444.02	r27_ch1_CEU_illumina:human_1m_beadchip
536	ss48403433	C/T	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch1_CEU_illumina:human_1m_beadchip
537	ss48403433	C/T	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	r27_ch1_CEU_illumina:human_1m_beadchip
579	ss48403433	C/T	CSHL-HAPMAP	HapMap-CEU	NA12815	CEPH1454.15	r27_ch1_CEU_illumina:human_1m_beadchip
5178	ss48403433	C/C	CSHL-HAPMAP	HapMap-HCB	NA18622	CH18622	r27_ch1_CHB_illumina:golden_gate_1.0.0
5241	ss48403433	C/C	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r27_ch1_YRI_illumina:human_1m_beadchip
5270	ss48403433	N/N	CSHL-HAPMAP	HapMap-YRI	NA19092	YOR040.03	r27_ch1_YRI_illumina:human_1m_beadchip
5309	ss48403433	C/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	r27_ch1_YRI_illumina:human_1m_beadchip

Genotype data submitted for	1055	samples from	1055	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
	UNKNOWN	UNKNOWN	UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .