Reference SNP(refSNP) Cluster Report: rs7180279

Reference SNP(refSNP) Cluster Report: rs7180279

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/130
Map to Genome Build:	36.3

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

HGVS Names
NG_008660.1:g.8238A>G
NM_198141.2:c.2543A>G
NM_198141.2:c.52A>G
NM_212464.2:c.-254A>G
NM_212465.2:c.-254A>G
NM_212467.2:c.-254A>G
NP_937784.2:p.Gln848Arg
NP_937784.2:p.Lys122Glu
NT_010194.16:g.13434095A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10796965 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7180279 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
ss10796965	BCM_SSAHASNP\|chr15.NT_010194.15_13433149	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	06/30/03	03/31/08	116	Genomic	unknown
ss19321049	CSHL-HAPMAP\|CSHL-HuDD-200402.chr15.NT_010194.16_13434095	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	02/20/04	03/04/04	120	Genomic	unknown
ss40575415	ABI\|hCV2110151	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	07/17/05	07/17/05	126	Genomic	unknown
ss65729230	ILLUMINA\|Human1-rs7180279	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	10/10/06	10/10/06	127	Genomic	unknown
ss66690218	ILLUMINA\|HumanHap300v1.1_rs7180279	fwd/B	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	11/09/06	11/09/06	127	Genomic	unknown
ss67552038	ILLUMINA\|HumanHap550v1.1_rs7180279	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	11/14/06	11/14/06	127	Genomic	unknown
ss67927072	ILLUMINA\|HumanHap650Yv1.0_rs7180279	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	11/14/06	11/15/06	127	Genomic	unknown
ss69174806	PERLEGEN\|PGP04779722	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	01/30/07	03/31/08	127	Genomic	unknown
ss70914124	ILLUMINA\|HumanHap550v3.0__rs7180279	rev/B	C/T	accacacacttgctgggataatgacccctc	ggtcagcaaaactggaatagatacaaacag	04/20/07	03/31/08	130	Genomic	unknown
ss71512436	ILLUMINA\|HumanHap650Yv3.0_rs7180279	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	04/23/07	04/23/07	127	Genomic	unknown
ss74812954	AFFY\|SNP_M-289022	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	08/09/07	08/09/07	128	Genomic	unknown
ss75595974	ILLUMINA\|ILMN_Human_1M_rs7180279	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	08/28/07	08/29/07	129	Genomic	unknown
ss79248883	ILLUMINA\|HumanHap300v2.0_rs7180279	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	04/18/07	11/18/07	130	Genomic	unknown
ss84631838	KRIBB_YJKIM\|KHS763781	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	12/04/07	12/07/07	130	Genomic	unknown
ss85395681	HGSV\|Cor18517_SNV_20070510.chr15_40430830	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	12/06/07	12/09/07	130	Genomic	unknown
ss118204279	ILLUMINA-UK\|NA18507_000026333_NCBI36.1_chr15_40430830	fwd/T	A/G	ctgtttgtatctattccagttttgctgacc	gaggggtcattatcccagcaagtgtgtggt	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 CCTTGGTACA CAGAGTTGTC tttttttttt ttttttttga gacggagttt tgctcttgtc
 gcccaggctg gagtgcagtg gcatgatctc agctcactgc aacctcagcc tcccgggttc
 aagcaattct cctgcctcag cctcctgagt agctgggatt acagatgccc accaccatgc
 ctggctaatt ttttgtattt ttttagtaga gacggggttt cgtcatgttg ggcaggctgg
 tctcgaactc ctgacctcaa gtgatccgcc cacgttggcc tcccaaagtg ctgggattac
 aggcatgagc caccatgccc agcGAGTCGT CTTttattat tattattatt attattttga
 gatggagtct cactgtatca cccagtctgg agtacagtgg tgcgatctca gctcactgca
 acctctatct cccaggttcg ggggattctc gtgtctcagc ctcccaagta gctgggacta
 caggcaccca ccaccactcc tggctaattt ttgtattttt agtatagaca ggattttgcc
 atgttgccca ggctggtgtt gaactcctgg cctcaagtga tctgcccacc tcggcctccc
 aaagtgctgg gattacaggc gtgagccacc gtgcctggGT CTTTTATTAT CTCTTCATCC
 TAGTAAATAT GACTCCCATA TGGATCATGC CTCCAAGGGA CAGATGGGAG AGGAACTCAC
 AAGGCTGGAG ATGTTGAGCT GGTGGCCACT TCAAACCCCC ATCCCTCTCC TTTTAATACT
 GTTTGTATCT ATTCCAGTTT TGCTGACC
 R
 GAGGGGTCAT TATCCCAGCA AGTGTGTGGT GGAGAAGATC TTGGTCTTAG GCTTCAGGAA
 GGAGCCATCT TCTGTGACTA CCCACTCATC TGGTGAGAAA GCAGTCCATT CTTACCTCAC
 CATTTGTTTT TATAAACAGA AGTATCTGCA GTGAGATGAT TAGTCCCCAA ACGGAGATAA
 TATGCTGAGC CTGAGTGTGT

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_010194

dbSNP Blast Analysis

UniGene Cluster ID
143261

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss10796965	HapMap-CEU	European	120	IG	0.933	0.067			0.967	0.033

	HapMap-HCB	Asian	90	IG	0.844	0.156			0.922	0.078

	HapMap-JPT	Asian	90	IG	0.933	0.067			0.967	0.033

	HapMap-YRI	Sub-Saharan African	120	IG	0.533	0.383	0.083		0.725	0.275

ss69174806	HapMap-CEU	European	118	GF	0.898	0.102			0.949	0.051

	HapMap-HCB	Asian	90	GF	0.711	0.289			0.856	0.144

	HapMap-JPT	Asian	90	GF	0.867	0.133			0.933	0.067

	HapMap-YRI	Sub-Saharan African	120	GF	0.317	0.683			0.658	0.342

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss10796965	1146	865	250	14

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs7180279	1207	865	250	14

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
150	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA10846	CEPH1334.01	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
151	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
199	ss10796965	A/G	CSHL-HAPMAP	HapMap-CEU	NA12056	CEPH1344.12	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
225	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
252	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
262	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
400	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
457	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA10839	CEPH1420.02	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
565	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
579	ss10796965	A/G	CSHL-HAPMAP	HapMap-CEU	NA12815	CEPH1454.15	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
611	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
620	ss10796965	A/A	CSHL-HAPMAP	HapMap-CEU	NA12874	CEPH1459.11	r27_ch15_CEU_illumina:human_1m_beadchip	5115525
5132	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18500	YOR004.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5137	ss10796965	G/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5140	ss10796965	G/G	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5141	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5145	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA19240	YOR117.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5148	ss10796965	A/A	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5157	ss10796965	N/N	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5171	ss10796965	A/A	CSHL-HAPMAP	HapMap-HCB	NA18563	CH18563	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5173	ss10796965	A/A	CSHL-HAPMAP	HapMap-HCB	NA18612	CH18612	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5174	ss10796965	A/A	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5182	ss10796965	A/G	CSHL-HAPMAP	HapMap-HCB	NA18577	CH18577	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5189	ss10796965	A/A	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5190	ss10796965	A/A	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	r27_ch15_CHB_illumina:human_1m_beadchip	5115525
5210	ss10796965	A/A	CSHL-HAPMAP	HapMap-JPT	NA18961	JA18961	r27_ch15_JPT_illumina:human_1m_beadchip	5115525
5222	ss10796965	A/A	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r27_ch15_JPT_illumina:human_1m_beadchip	5115525
5225	ss10796965	A/A	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r27_ch15_JPT_illumina:human_1m_beadchip	5115525
5237	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18501	YOR004.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5238	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5241	ss10796965	G/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5244	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5245	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5250	ss10796965	N/N	CSHL-HAPMAP	HapMap-YRI	NA18521	YOR016.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5252	ss10796965	N/N	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5254	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5255	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18871	YOR017.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5258	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18853	YOR018.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5262	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18863	YOR024.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5264	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5265	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5269	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19093	YOR040.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5270	ss10796965	N/N	CSHL-HAPMAP	HapMap-YRI	NA19092	YOR040.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5271	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19103	YOR042.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5272	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5273	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19101	YOR042.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5274	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5276	ss10796965	G/G	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5277	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5280	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA19173	YOR047.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5283	ss10796965	N/N	CSHL-HAPMAP	HapMap-YRI	NA19205	YOR048.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5285	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5287	ss10796965	G/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5290	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5291	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA19207	YOR051.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5292	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19161	YOR056.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5297	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5304	ss10796965	A/G	CSHL-HAPMAP	HapMap-YRI	NA19154	YOR072.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5307	ss10796965	N/N	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5308	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19143	YOR074.02	r27_ch15_YRI_illumina:human_1m_beadchip	5115525
5309	ss10796965	A/A	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	r27_ch15_YRI_illumina:human_1m_beadchip	5115525

Genotype data submitted for	1207	samples from	1207	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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .