Reference SNP(refSNP) Cluster Report: rs12939811

Reference SNP(refSNP) Cluster Report: rs12939811

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/130
Map to Genome Build:	36.3

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

HGVS Names
NM_002144.3:c.309A>T
NM_002144.3:c.318A>T
NP_002135.2:p.Gln103His
NT_010783.14:g.5261236T>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss40827510 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12939811 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
ss21386885	SSAHASNP\|WGSA-200403-chr17.chr17.NT_010783.14_5261236	fwd/T	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	03/19/04	03/19/04	121	Genomic	unknown
ss40827510	ABI\|hCV7945824	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	07/17/05	11/03/06	126	Genomic	unknown
ss48425486	APPLERA_GI\|hCV7945824	rev/	A/T	cgggccttctcagtactaccctctgggtca	tcagaaggagacggaggctattttcatccc	09/28/05	11/03/06	126	Genomic	unknown
ss69197146	PERLEGEN\|PGP07782510	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	01/30/07	03/31/08	127	Genomic	unknown
ss74816079	AFFY\|SNP_M-311172	fwd/T	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	08/09/07	08/09/07	128	Genomic	unknown
ss74899750	ILLUMINA\|ILMN_Human_1M_rs12939811	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	08/28/07	08/29/07	129	Genomic	unknown
ss76588636	AFFY\|AFFY_6_1M_SNP_A-8449715	rev/	A/T	actaccctctgggtca	tcagaaggagacggag	08/28/07	08/30/07	129	Genomic	unknown
ss78374977	HGSV\|Cor12878_SNV_20070510.chr17_43962957	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	10/17/07	10/19/07	129	Genomic	unknown
ss90604931	BCMHGSC_JDW\|JWB-1026953	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	02/26/08	02/29/08	129	Genomic	unknown
ss96597918	HUMANGENOME_JCVI\|1103645336323	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	03/26/08	03/26/08	130	Genomic	unknown
ss109788096	1000GENOMES\|CEU.trio.12.15.2008_3404656_chr17_43962957	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	12/15/08	12/16/08	130	Genomic	unknown
ss113580741	1000GENOMES\|NA19240_2008_12_16_3063876_chr17_43962957	fwd/	A/T	gggatgaaaatagcctccgtctccttctga	tgacccagagggtagtactgagaaggcccg	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 CCGGAGAAGG GGTGGCCACA TCTGAGCCCT ACCTGTCTTG GGTGGGTTTC TCTTAACCTT
 CATCCAGTCG AAGGTCCGGG CCGTGGGGGT GTTAGGTTCT GAAGGGCAGG GTGTTTCCTT
 GTCCTCGGAG AGGAGATCAG CATAGGCCGG TGCAAAGCTT GCGGTCTGCT CGTTCCCATA
 AGGGGGATGC TGCGGAGGAT ATGGCCCCGG ACCGGCTCCA CCTGCTCCGT AGCCATCGGA
 CAAGCCCCCT AGCTGGGCCC CGTAGCTCGA GGGATGAAAA TAGCCTCCGT CTCCTTCTGA
 W
 TGACCCAGAG GGTAGTACTG AGAAGGCCCG TAGCTGGGGC TGCAGGCGGC AGGAGCATAC
 CCCGAGGGCG CAGAGCTGGG GAAGGGCACC CCCAGGGTCG AAGGCGGCTG CTGGGCGGGA
 TAGCCGGAGT TCTGCTGAAA CGCAGGGCTG GACAGCCCCC CACCGTAGCG GCCCTCGCTT
 GCATAGCTGT CAACCGCCTG AGCCGAGCTT GGGGGAAAGG AGGTTGGGGC GCTGTGGGCG
 CTGTGGGCGC TGTAGGCGCT GGGTCCCCGG TTACAGAGTG GGTACTCTAA GAAGGAGTTC

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_010783 ABBA01041170

dbSNP Blast Analysis

UniGene Cluster ID
99992

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss40827510	HapMap-CEU	European	112	IG	0.036	0.232	0.732	0.479	0.152	0.848

	HapMap-HCB	Asian	86	IG		0.070	0.930	1.000	0.035	0.965

	HapMap-JPT	Asian	88	IG		0.023	0.977	1.000	0.011	0.989

	HapMap-YRI	Sub-Saharan African	118	IG		0.153	0.847	0.527	0.076	0.924

	AoD_African_American		90	AF					0.090	0.910

	AoD_Caucasian		92	AF					0.170	0.830

ss48425486	AGI_ASP population	multiple	74	IG	0.054	0.297	0.649	0.655	0.203	0.797

ss69197146	HapMap-CEU	European	120	GF		0.183	0.817		0.092	0.908

	HapMap-HCB	Asian	90	GF		0.089	0.911		0.044	0.956

	HapMap-JPT	Asian	90	GF		0.022	0.978		0.011	0.989

	HapMap-YRI	Sub-Saharan African	120	GF		0.100	0.900		0.050	0.950

Concordant Genotype	Total Sample	A/A	A/T	T/T
ss40827510	1191	12	196	962
ss48425486	38	24	11	2
ss96597918	1		1

RefSNP Genotype Summary	Total Individual	A/A	A/T	T/T
rs12939811	1246	36	208	964

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
214	ss40827510	A/T	CSHL-HAPMAP	HapMap-CEU	NA07345	CEPH1345.13	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
225	ss40827510	A/T	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
255	ss40827510	A/A	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
264	ss40827510	A/T	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
265	ss40827510	A/A	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
348	ss40827510	N/N	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
465	ss40827510	N/N	CSHL-HAPMAP	HapMap-CEU	NA12004	CEPH1420.10	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
535	ss40827510	A/T	CSHL-HAPMAP	HapMap-CEU	NA12750	CEPH1444.13	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
611	ss40827510	A/A	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
620	ss40827510	A/A	CSHL-HAPMAP	HapMap-CEU	NA12874	CEPH1459.11	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
621	ss40827510	A/T	CSHL-HAPMAP	HapMap-CEU	NA12875	CEPH1459.12	r27_ch17_CEU_illumina:human_1m_beadchip	5372077
5140	ss40827510	A/T	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	r27_ch17_YRI_illumina:human_1m_beadchip	5372077
5265	ss40827510	A/T	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	r27_ch17_YRI_illumina:human_1m_beadchip	5372077
5275	ss40827510	A/T	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r27_ch17_YRI_illumina:human_1m_beadchip	5372077
5277	ss40827510	A/T	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r27_ch17_YRI_illumina:human_1m_beadchip	5372077
5278	ss40827510	A/T	CSHL-HAPMAP	HapMap-YRI	NA19201	YOR045.02	r27_ch17_YRI_illumina:human_1m_beadchip	5372077

Genotype data submitted for	1246	samples from	1246	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

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Revised: May 25, 2006 1:38 PM .