Reference SNP(refSNP) Cluster Report: rs11617079

Reference SNP(refSNP) Cluster Report: rs11617079

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/130
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_013238.2:c.103A>G
NP_037370.2:p.Arg35Gly
NT_024524.13:g.24577865A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76886425 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11617079 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
ss16608598	CSHL-HAPMAP\|CSHL-HuAA-200402.chr13.NT_024524.13_24577865	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	02/17/04	10/26/06	120	Genomic	unknown
ss28510643	MGC_GENOME_DIFF\|BC010910x37546841-A24577865G	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	08/25/04	08/25/04	126	cDNA	unknown
ss43504407	ABI\|hCV25758175	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	07/18/05	07/18/05	126	Genomic	unknown
ss48426449	APPLERA_GI\|hCV25758175	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	09/28/05	11/03/06	126	Genomic	unknown
ss66668408	ILLUMINA\|HumanHap300v1.1_rs11617079	fwd/B	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	11/09/06	11/09/06	127	Genomic	unknown
ss66936581	ILLUMINA\|HumanHap550v1.1_rs11617079	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	11/14/06	11/14/06	127	Genomic	unknown
ss67097152	ILLUMINA\|HumanHap650Yv1.0_rs11617079	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	11/14/06	11/14/06	127	Genomic	unknown
ss69133053	PERLEGEN\|PGP04781020	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	01/30/07	03/31/08	127	Genomic	unknown
ss70395597	ILLUMINA\|HumanHap300v2.0_rs11617079	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	04/18/07	11/18/07	127	Genomic	unknown
ss70532315	ILLUMINA\|HumanHap550v3.0__rs11617079	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	04/20/07	03/30/08	130	Genomic	unknown
ss71063168	ILLUMINA\|HumanHap650Yv3.0_rs11617079	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	04/23/07	04/23/07	127	Genomic	unknown
ss75564268	ILLUMINA\|ILMN_Human_1M_rs11617079	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	08/28/07	08/29/07	129	Genomic	unknown
ss76886425	SI_EXO\|NT_024524.13_24577865	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	09/20/07	09/20/07	129	Genomic	unknown
ss85106471	KRIBB_YJKIM\|KHS900634	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	12/04/07	12/08/07	130	Genomic	unknown
ss86347419	CANCER-GENOME\|16384	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	01/25/08	01/25/08	129	Genomic	unknown
ss114625294	1000GENOMES\|NA19240_2008_12_16_2595679_chr13_42495865	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	12/18/08	12/18/08	130	Genomic	unknown
ss118569947	ILLUMINA-UK\|NA18507_000035515_NCBI36.1_chr13_42495865	fwd/T	A/G	aaacggccagacgccgacgtcgaccagcag	gactggtgagtcctgccagcggcccccacc	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 GGAGGGACCA GGCCCAAGTA TATAAAGCTC CCTGAGGGTC CGCGTTGGCT TTGCGCCTGT
 GAGTGTGATT CAAGAACGTC CCAGTGCCCT TGGCTCCTTT CGGAGTGTGA CCCCGTGCTT
 GCACGGGACA CGTTACCCAG CTCGGGTGAG AAGGGTATCT TCCGGGAACC TCGCCTTTAA
 TAGCACAACG AGCGCAGAGT CCACTGGATC TGCGAGAAGA AACCGCGCTA ACTAGTTTGT
 CCCTACGGCC GCCTCGTAGT CACTGCCGCG GCGCCTTGAG TCTCCGGGCC GCCTTGCCAT
 GGCTGCCCGT GGTGTCATCG CTCCAGTTGG CGAGAGTTTG CGCTACGCTG AGTACTTGCA
 GCCCTCGGCC AAACGGCCAG ACGCCGACGT CGACCAGCAG
 R
 GACTGGTGAG TCCTGCCAGC GGCCCCCACC CCTCTCTGGC TCCCTTGTAG TTTCTGCTTC
 AGCCCCCTCT ACCGCCTCAC CCTTGAACCT TTGTACTCCC CCGCATTCGC TCACGGTCTG
 TGCCCTAGCG CTCACTTGTT CAGTGGAGAG ACCGCTTTGT GCTGGGCTTT GACGCCTGGG
 CGTGGAAGAC GGAGCAGTTC TGAGGATCTG TCTCCTCAAG GAGCTTCCAG TCTTGTCTGG
 GACACAAACC AGAAAACAGG CAATTGCAAA TACAGTAAAA TAAGTGCTGT ATGTGGATTT
 TCCTATCTCA TAGGAGGCCC TAAAAACGTC TTGCAGGGGA CGTGGTGGGA TCAGGGACGC
 TTCTTGGAGA AAGCTGTAGT TAAAAATTAA GATCTGAATG

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_024524.13 BC010910

dbSNP Blast Analysis

UniGene Cluster ID
438830

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss16608598	HapMap-CEU	European	118	IG	0.576	0.356	0.068	1.000	0.754	0.246

	HapMap-HCB	Asian	90	IG	0.711	0.289		0.273	0.856	0.144

	HapMap-JPT	Asian	90	IG	0.778	0.222			0.889	0.111

	HapMap-YRI	Sub-Saharan African	120	IG	0.333	0.533	0.133	0.403	0.600	0.400

ss48426449	AGI_ASP population	multiple	76	IG	0.579	0.316	0.105	0.254	0.737	0.263

ss69133053	HapMap-CEU	European	120	GF	0.633	0.350	0.017		0.808	0.192

	HapMap-HCB	Asian	90	GF	0.844	0.156			0.922	0.078

	HapMap-JPT	Asian	90	GF	0.844	0.156			0.922	0.078

	HapMap-YRI	Sub-Saharan African	118	GF	0.542	0.390	0.068		0.737	0.263

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss48426449	39	22	12	4
ss76886425	1165	727	352	68

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs11617079	1246	749	364	72

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
213	ss76886425	G/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	r27_ch13_CEU_illumina:human_1m_beadchip
215	ss76886425	N/N	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r27_ch13_CEU_illumina:human_1m_beadchip
225	ss76886425	A/G	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch13_CEU_illumina:human_1m_beadchip
226	ss76886425	G/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch13_CEU_illumina:human_1m_beadchip
239	ss76886425	A/G	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	r27_ch13_CEU_illumina:human_1m_beadchip
265	ss76886425	A/A	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	r27_ch13_CEU_illumina:human_1m_beadchip
348	ss76886425	N/N	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r27_ch13_CEU_illumina:human_1m_beadchip
439	ss76886425	G/G	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	r27_ch13_CEU_illumina:human_1m_beadchip
524	ss76886425	A/A	CSHL-HAPMAP	HapMap-CEU	NA12740	CEPH1444.02	r27_ch13_CEU_illumina:human_1m_beadchip
5133	ss76886425	N/N	CSHL-HAPMAP	HapMap-YRI	NA18502	YOR004.02	r27_ch13_YRI_illumina:human_1m_beadchip
5135	ss76886425	G/G	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	r27_ch13_YRI_illumina:human_1m_beadchip
5139	ss76886425	N/N	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r27_ch13_YRI_illumina:human_1m_beadchip
5140	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	r27_ch13_YRI_illumina:human_1m_beadchip
5142	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r27_ch13_YRI_illumina:human_1m_beadchip
5144	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r27_ch13_YRI_illumina:human_1m_beadchip
5149	ss76886425	A/G	CSHL-HAPMAP	HapMap-HCB	NA18524	CH18524	r27_ch13_CHB_illumina:human_1m_beadchip
5151	ss76886425	A/G	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	r27_ch13_CHB_illumina:human_1m_beadchip
5160	ss76886425	A/G	CSHL-HAPMAP	HapMap-HCB	NA18545	CH18545	r27_ch13_CHB_illumina:human_1m_beadchip
5165	ss76886425	A/G	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r27_ch13_CHB_illumina:human_1m_beadchip
5187	ss76886425	A/G	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	r27_ch13_CHB_illumina:human_1m_beadchip
5191	ss76886425	A/G	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	r27_ch13_CHB_illumina:human_1m_beadchip
5212	ss76886425	A/G	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	r27_ch13_JPT_illumina:human_1m_beadchip
5221	ss76886425	A/G	CSHL-HAPMAP	HapMap-JPT	NA18995	JA18995	r27_ch13_JPT_illumina:human_1m_beadchip
5235	ss76886425	A/G	CSHL-HAPMAP	HapMap-JPT	NA19007	JA19007	r27_ch13_JPT_illumina:human_1m_beadchip
5240	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r27_ch13_YRI_illumina:human_1m_beadchip
5241	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r27_ch13_YRI_illumina:human_1m_beadchip
5242	ss76886425	G/G	CSHL-HAPMAP	HapMap-YRI	NA18508	YOR009.02	r27_ch13_YRI_illumina:human_1m_beadchip
5244	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	r27_ch13_YRI_illumina:human_1m_beadchip
5245	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	r27_ch13_YRI_illumina:human_1m_beadchip
5251	ss76886425	N/N	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	r27_ch13_YRI_illumina:human_1m_beadchip
5254	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	r27_ch13_YRI_illumina:human_1m_beadchip
5256	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	r27_ch13_YRI_illumina:human_1m_beadchip
5259	ss76886425	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r27_ch13_YRI_illumina:human_1m_beadchip
5262	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18863	YOR024.01	r27_ch13_YRI_illumina:human_1m_beadchip
5264	ss76886425	G/G	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	r27_ch13_YRI_illumina:human_1m_beadchip
5265	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	r27_ch13_YRI_illumina:human_1m_beadchip
5267	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r27_ch13_YRI_illumina:human_1m_beadchip
5287	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r27_ch13_YRI_illumina:human_1m_beadchip
5290	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	r27_ch13_YRI_illumina:human_1m_beadchip
5294	ss76886425	G/G	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r27_ch13_YRI_illumina:human_1m_beadchip
5295	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r27_ch13_YRI_illumina:human_1m_beadchip
5296	ss76886425	A/G	CSHL-HAPMAP	HapMap-YRI	NA19222	YOR058.02	r27_ch13_YRI_illumina:human_1m_beadchip

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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .