Reference SNP(refSNP) Cluster Report: rs1139971

Reference SNP(refSNP) Cluster Report: rs1139971

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:	Not available
Clinical Association:	unknown

HGVS Names
NM_001024844.1:c.646A>G
NM_002231.3:c.721A>G
NP_001020015.1:p.Ile216Val
NP_002222.1:p.Ile241Val
NT_009237.17:g.43427509A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss20761986 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1139971 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
ss1549682	LEE\|1103523	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgagctcctggggatggtcctgtccatct	09/13/00	10/10/03	86	cDNA	unknown
ss4433743	LEE\|e1103524	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgagctcctggggatggtcctgtccatct	04/26/02	10/10/03	108	cDNA	unknown
ss16229386	CGAP-GAI\|1466874	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgagctcctggggatggtcctgtccatct	11/18/03	11/22/03	126	cDNA	unknown
ss20761986	SSAHASNP\|WGSA-200403-chr11.chr11.NT_009237.16_43404208	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	03/19/04	10/26/06	126	Genomic	unknown
ss24812526	SEQUENOM\|sqnm202365	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgagctcctggggatggtcctgtccatct	06/18/04	06/18/04	126	cDNA	unknown
ss28497245	MGC_GENOME_DIFF\|37541814-A43404208G	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	08/20/04	08/20/04	126	cDNA	unknown
ss28511877	MGC_GENOME_DIFF\|BC000726x37541814-A43404208G	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	08/25/04	08/25/04	126	cDNA	unknown
ss28511958	MGC_GENOME_DIFF\|BC001821x37541814-A43404208G	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	08/25/04	08/25/04	126	cDNA	unknown
ss67039793	ILLUMINA\|HumanHap550v1.1_rs12790100	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	11/14/06	11/14/06	127	Genomic	unknown
ss67364281	ILLUMINA\|HumanHap650Yv1.0_rs12790100	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	11/14/06	11/14/06	127	Genomic	unknown
ss68139009	ILLUMINA\|HumanHap250Sv1.0_rs12790100	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	12/06/06	12/07/06	127	Genomic	unknown
ss69317155	PERLEGEN\|PGP05473085	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	01/30/07	08/14/07	127	Genomic	unknown
ss70585074	ILLUMINA\|HumanHap550v3.0__rs1139971	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	04/20/07	03/30/08	130	Genomic	unknown
ss71127876	ILLUMINA\|HumanHap650Yv3.0_rs1139971	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	04/23/07	04/23/07	127	Genomic	unknown
ss75568096	ILLUMINA\|ILMN_Human_1M_rs1139971	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	08/28/07	08/29/07	129	Genomic	unknown
ss83687627	KRIBB_YJKIM\|KHS519591	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	12/04/07	12/05/07	130	Genomic	unknown
ss88564376	BCMHGSC_JDW\|JWB-0416216	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	02/26/08	02/27/08	129	Genomic	unknown
ss97384025	HUMANGENOME_JCVI\|1103649674486	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	03/29/08	03/29/08	130	Genomic	unknown
ss110430366	1000GENOMES\|CEU.trio.12.15.2008_2541134_chr11_44596844	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	12/15/08	12/17/08	130	Genomic	unknown
ss114562197	1000GENOMES\|NA19240_2008_12_16_2287693_chr11_44596844	fwd/T	A/G	atcctcggcgtgggcgtgggtgtggccatc	tcgaggtctgagccccctcccccatccctt	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 AAGGAACAGG CAGAGCCCTC TGTAGGGGCT TCCGGGCTGG GACTGGGGGG CTCTCGGTGG
 TTCTGCATGG CGGGGTGGGA TGGTGCAGAG CGGGGTGATG TGACCGCATT CTGCCCTTGC
 AGGGCTGCAT GGAGAAGGTG CAGGCGTGGC TGCAGGAGAA CCTGGGCATC ATCCTCGGCG
 TGGGCGTGGG TGTGGCCATC
 R
 TCGAGGTCTG AGCCCCCTCC CCCATCCCTT CTCCATCCCA GGTCCTCCTG GGTTGTCTCT
 GTTCTGCTGA TCTCCTTGGG GAGGTGGTGG CCAAGGGGGC CAGCACCCCA TCAGCTTCCA
 GAGGCCCtct ggtctgagca ctgtctggct gtgtgacctc agacaaggca ctgccccgct
 ctgggcctcC CTCTGCTGCC TGCATCACAG GGTGGTTGTG AGGCTCAAGT TGAGGATCCA
 CTTAATCCCC ATGTAAACCT GGATGGTGAG GCTGGGGCGT CTGAGGCCGG GACACCCAGC
 CTCCCTCTGA CTCTCCGCC

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
sqnm202365	U20770 ABBA01060770 BC000726 BC001821 BG328568 Hs.25409

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss20761986	HapMap-CEU	European	120	IG	0.100	0.450	0.450	1.000	0.325	0.675

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

	HapMap-JPT	Asian	80	IG	0.275	0.500	0.225	1.000	0.525	0.475

	HapMap-YRI	Sub-Saharan African	114	IG	0.368	0.491	0.140	1.000	0.614	0.386

ss69317155	HapMap-CEU	European	120	GF	0.100	0.450	0.450		0.325	0.675

	HapMap-HCB	Asian	90	GF	0.333	0.444	0.222		0.556	0.444

	HapMap-JPT	Asian	88	GF	0.318	0.477	0.205		0.557	0.443

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

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss20761986	1202	295	557	327
ss69317155	265	74	118	72
ss97384025	1			1

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1139971	1208	302	566	335

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
226	ss20761986	G/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch11_CEU_illumina:human_1m_beadchip	4527431
226	ss69317155	A/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	chr11-HapMap-CEU
374	ss20761986	G/G	CSHL-HAPMAP	HapMap-CEU	NA12234	CEPH1375.12	r27_ch11_CEU_illumina:human_1m_beadchip	4527431
374	ss69317155	G/G	CSHL-HAPMAP	HapMap-CEU	NA12234	CEPH1375.12	chr11-HapMap-CEU
5172	ss20761986	G/G	CSHL-HAPMAP	HapMap-HCB	NA18570	CH18570	r27_ch11_CHB_illumina:human_1m_beadchip	4527431
5172	ss69317155	G/G	CSHL-HAPMAP	HapMap-HCB	NA18570	CH18570	chr11-HapMap-HCB
5236	ss20761986	N/N	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	r27_ch11_JPT_illumina:human_1m_beadchip	4527431
5236	ss69317155	A/G	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	chr11-HapMap-JPT
5295	ss20761986	A/A	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r27_ch11_YRI_illumina:human_1m_beadchip	4527431
5295	ss69317155	A/A	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	chr11-HapMap-YRI

Genotype data submitted for	1208	samples from	1208	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

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Revised: May 25, 2006 1:38 PM .