Reference SNP(refSNP) Cluster Report: rs2066480

Reference SNP(refSNP) Cluster Report: rs2066480

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	94/130
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_008157.1:g.5139G>A
NM_000197.1:c.91G>A
NP_000188.1:p.Val31Ile
NT_008470.18:g.6385501C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss12584142 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2066480 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	Ancestral Allele	Success Rate
ss2978077	UWGC\|hsd17b3-e1+t64	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	01/30/01	04/07/04	94	Genomic		unknown
ss3188834	HGBASE\|SNP000064603	fwd/T	A/G	gaagtgcgtgagattctccagatgt	ttttactgaactactggaaagtttt	07/23/01	10/10/03	98	cDNA		unknown
ss12584142	EGP_SNPS\|HSD17B3-001116	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	07/23/03	04/07/04	117	Genomic		unknown
ss24077237	PERLEGEN\|afd4520086	rev/B	C/T	ttggcaaaactttccagtagttcagtaaaa	acatctggagaatctcacgcacttcgccag	08/10/04	09/13/04	123	Genomic		unknown
ss38339080	CEPH\|G7-SN-E1S4	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	05/11/05	05/11/05	125	Genomic	A	100 %
ss66860310	EGP_SNPS\|HSD17B3_001116	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	11/09/06	12/16/06	127	Genomic		unknown
ss67221499	ILLUMINA\|HumanHap550v1.1_rs2066480	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	11/14/06	11/14/06	127	Genomic		unknown
ss67615858	ILLUMINA\|HumanHap650Yv1.0_rs2066480	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	11/14/06	11/14/06	127	Genomic		unknown
ss68195492	ILLUMINA\|HumanHap250Sv1.0_rs2066480	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	12/06/06	12/07/06	127	Genomic		unknown
ss69296756	PERLEGEN\|PGP04520086	rev/B	C/T	ttggcaaaactttccagtagttcagtaaaa	acatctggagaatctcacgcacttcgccag	01/30/07	08/14/07	127	Genomic		unknown
ss70699791	ILLUMINA\|HumanHap550v3.0__rs2066480	rev/B	C/T	ttggcaaaactttccagtagttcagtaaaa	acatctggagaatctcacgcacttcgccag	04/20/07	03/30/08	130	Genomic		unknown
ss71265754	ILLUMINA\|HumanHap650Yv3.0_rs2066480	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	04/23/07	04/23/07	127	Genomic		unknown
ss74810524	AFFY\|SNP_M-184169	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	08/09/07	08/09/07	128	Genomic		unknown
ss75430489	ILLUMINA\|ILMN_Human_1M_rs2066480	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	08/28/07	08/29/07	129	Genomic		unknown
ss76738304	AFFY\|AFFY_6_1M_SNP_A-8599619	rev/B	C/T	cagtagttcagtaaaa	acatctggagaatctc	08/28/07	08/30/07	129	Genomic		unknown
ss83962882	KRIBB_YJKIM\|KHS585662	fwd/T	A/G	ctggcgaagtgcgtgagattctccagatgt	ttttactgaactactggaaagttttgccaa	12/04/07	12/06/07	130	Genomic		unknown

Fasta sequence (Legend)

 CAGAGGATTA TGTAAAGAAG TTACTTTAAT CTAGATGCCC CTGACTTGAT GGAACACGTC
 CAGTGACTCC TGGAAGAAGA TCTGGAGGTC TCCAGAGCAG CGTGGTCCCA GGAGGCATAC
 ACAGAGAGCC ACGGCCAGGG CTGAAACAGT CTGTTGAGTG CAGCCATGGG GGACGTCCTG
 GAACAGTTCT TCATCCTCAC AGGGCTGCTG GTGTGCCTGG CCTGCCTGGC GAAGTGCGTG
 AGATTCTCCA GATGT
 R
 TTTTACTGAA CTACTGGAAA GTTTTGCCAA AGTCTTTCTT GCGGTCAATG GGACAGTGGG
 CAGGTAAGGG AGTGTTCCAT CTCATGTTTT TTTTGCTGCT GTTGTTCCTG CTTGTTACTA
 TTATTATTAt ttttgagaca gacacttgct ctgtcaccca ggctggagtg caatggcgcg
 atcttggctc actgcaacct ccgcttcccg ggtttaagca attctcctgc ctcagcctcc
 caagtagctg ggatt

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
G67554	NM_000197,AL

dbSNP Blast Analysis

UniGene Cluster ID
477

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss12584142	PDR90	Global	174	IG	0.057	0.943	1.000	0.029	0.971

	HapMap-CEU	European	120	IG	0.017	0.983	1.000	0.008	0.992

	HapMap-HCB	Asian	90	IG	0.222	0.778	0.403	0.111	0.889

	HapMap-JPT	Asian	88	IG	0.136	0.864	0.655	0.068	0.932

	HapMap-YRI	Sub-Saharan African	120	IG		1.000			1.000

	COHORT_CONSORTIUM_B		76	AF				0.026	0.974

	COHORT_CONSORTIUM_C		76	AF				0.013	0.987

	COHORT_CONSORTIUM_H		76	AF				0.014	0.986

	COHORT_CONSORTIUM_J		76	AF				0.066	0.934

	COHORT_CONSORTIUM_L		76	AF					1.000

	CEPH-TRIOS		606	AF				0.003	0.997

ss24077237	AFD_EUR_PANEL	European	48	IG		1.000			1.000

	AFD_AFR_PANEL	African American	46	IG		1.000			1.000

	AFD_CHN_PANEL	Asian	48	IG	0.167	0.833	0.752	0.083	0.917

ss2978077	NIHPDR	Global	74	IG	0.054	0.946	1.000	0.027	0.973

ss66860310	HSP_GENO_PANEL		54	IG		1.000			1.000

	CEU_GENO_PANEL	European	68	IG		1.000			1.000

	AAM_GENO_PANEL	African American	124	IG	0.016	0.984	1.000	0.008	0.992

	CHB_GENO_PANEL	Asian	90	IG	0.222	0.778	0.403	0.111	0.889

	YRI_GENO_PANEL	Sub-Saharan African	120	IG		1.000			1.000

	JPT_GENO_PANEL	Asian	24	IG	0.083	0.917	1.000	0.042	0.958

ss69296756	HapMap-CEU	European	118	GF	0.085	0.915		0.042	0.958

	HapMap-HCB	Asian	90	GF	0.289	0.711		0.144	0.856

	HapMap-JPT	Asian	90	GF	0.200	0.800		0.100	0.900

	HapMap-YRI	Sub-Saharan African	120	GF	0.050	0.950		0.025	0.975

Concordant Genotype	Total Sample	A/G	G/G
ss12584142	1114	56	951
ss24077237	69
ss2978077	37	2	35
ss66860310	319	12	220

RefSNP Genotype Summary	Total Individual	A/G	G/G
rs2066480	1316	58	1042

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
174	ss12584142	N/N	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
262	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
262	ss66860310	N/N	EGP_SNPS	CEU_GENO_PANEL	NA11829	NA11829	HSD17B3-CEU-041206
335	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA12707	CEPH1358.01	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
363	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA11995	CEPH1362.16	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
363	ss66860310	G/G	EGP_SNPS	CEU_GENO_PANEL	NA11995	NA11995	HSD17B3-CEU-041206
399	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
399	ss24077237	C/C	PERLEGEN	AFD_EUR_PANEL	NA10830		71_IND_CHR_9
400	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
400	ss24077237	C/C	PERLEGEN	AFD_EUR_PANEL	NA10831		71_IND_CHR_9
429	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
524	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA12740	CEPH1444.02	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
536	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
536	ss66860310	G/G	EGP_SNPS	CEU_GENO_PANEL	NA12751	NA12751	HSD17B3-CEU-041206
538	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
548	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
548	ss66860310	N/N	EGP_SNPS	CEU_GENO_PANEL	NA12763	NA12763	HSD17B3-CEU-041206
611	ss12584142	G/G	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	r27_ch9_CEU_affymetrix:genomewidesnp_6.0	683034
5142	ss12584142	G/G	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r27_ch9_YRI_illumina:golden_gate_1.1.0	683034
5143	ss12584142	G/G	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	r27_ch9_YRI_illumina:golden_gate_1.1.0	683034
5143	ss66860310	G/G	EGP_SNPS	YRI_GENO_PANEL	NA19193	NA19193	HSD17B3-YRI-041206
5155	ss12584142	G/G	CSHL-HAPMAP	HapMap-HCB	NA18537	CH18537	r27_ch9_CHB_affymetrix:genomewidesnp_6.0	683034
5155	ss66860310	G/G	EGP_SNPS	CHB_GENO_PANEL	NA18537	NA18537	HSD17B3-CHB-041206
5166	ss12584142	G/G	CSHL-HAPMAP	HapMap-HCB	NA18552	CH18552	r27_ch9_CHB_affymetrix:genomewidesnp_6.0	683034
5166	ss66860310	G/G	EGP_SNPS	CHB_GENO_PANEL	NA18552	NA18552	HSD17B3-CHB-041206
5190	ss12584142	G/G	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	r27_ch9_CHB_affymetrix:genomewidesnp_6.0	683034
5190	ss66860310	G/G	EGP_SNPS	CHB_GENO_PANEL	NA18636	NA18636	HSD17B3-CHB-041206
5201	ss12584142	G/G	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r27_ch9_JPT_affymetrix:genomewidesnp_6.0	683034
5201	ss66860310	N/N	EGP_SNPS	JPT_GENO_PANEL	NA18948	NA18948	HSD17B3-JPT-041206
5224	ss12584142	G/G	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	r27_ch9_JPT_affymetrix:genomewidesnp_6.0	683034
5224	ss66860310	N/N	EGP_SNPS	JPT_GENO_PANEL	NA18974	NA18974	HSD17B3-JPT-041206
5236	ss12584142	N/N	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	r27_ch9_JPT_affymetrix:genomewidesnp_6.0	683034
5236	ss66860310	N/N	EGP_SNPS	JPT_GENO_PANEL	NA19003	NA19003	HSD17B3-JPT-041206
5241	ss12584142	G/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r27_ch9_YRI_illumina:golden_gate_1.1.0	683034
5263	ss12584142	G/G	CSHL-HAPMAP	HapMap-YRI	NA18861	YOR024.02	r27_ch9_YRI_illumina:golden_gate_1.1.0	683034
5263	ss66860310	G/G	EGP_SNPS	YRI_GENO_PANEL	NA18861	NA18861	HSD17B3-YRI-041206
5276	ss12584142	G/G	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	r27_ch9_YRI_illumina:golden_gate_1.1.0	683034
5276	ss66860310	G/G	EGP_SNPS	YRI_GENO_PANEL	NA19138	NA19138	HSD17B3-YRI-041206

Genotype data submitted for	1577	samples from	1316	individuals	Individual with multiple genotypes submission:	261

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .