Reference SNP(refSNP) Cluster Report: rs2073478

Reference SNP(refSNP) Cluster Report: rs2073478

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_000692.3:c.320G>T
NP_000683.3:p.Arg107Leu
NT_008413.17:g.38386065G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76892366 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2073478 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
ss2987805	YUSUKE\|IMS-JST009830	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	05/24/01	10/25/06	96	Genomic	unknown
ss3172732	WIAF-CSNP\|WIAF-12910	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	06/19/01	04/07/04	98	cDNA	unknown
ss3188552	HGBASE\|SNP000574136	fwd/B	G/T	tctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggat	07/09/01	10/10/03	98	Genomic	unknown
ss6312103	RIKENSNPRC\|ssj0004485	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	01/15/03	10/10/03	111	Genomic	unknown
ss16260355	CGAP-GAI\|1520943	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	11/18/03	11/22/03	120	cDNA	unknown
ss19799525	CSHL-HAPMAP\|CSHL-HuDD-200402.chr9.NT_008413.16_38386065	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	02/20/04	05/16/04	120	Genomic	unknown
ss22819491	SSAHASNP\|WGSA-200403-chr9.chr9.NT_008413.16_38386065	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	03/21/04	03/21/04	121	Genomic	unknown
ss23587937	PERLEGEN\|afd4098016	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	08/10/04	09/13/04	123	Genomic	unknown
ss28497300	MGC_GENOME_DIFF\|37540361-G38386065T	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	08/20/04	08/20/04	126	cDNA	unknown
ss28511941	MGC_GENOME_DIFF\|BC001619x37540361-G38386065T	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	08/25/04	08/25/04	126	cDNA	unknown
ss48430137	APPLERA_GI\|hCV15950964	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	10/02/05	11/03/06	126	Genomic	unknown
ss65726181	ILLUMINA\|Human1-rs2073478	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	10/10/06	10/10/06	127	Genomic	unknown
ss66643182	ILLUMINA\|HumanHap300v1.1_rs2073478	fwd/T	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	11/09/06	11/09/06	127	Genomic	unknown
ss67222488	ILLUMINA\|HumanHap550v1.1_rs2073478	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	11/14/06	11/14/06	127	Genomic	unknown
ss67616943	ILLUMINA\|HumanHap650Yv1.0_rs2073478	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	11/14/06	11/14/06	127	Genomic	unknown
ss68395255	CSHL-HAPMAP\|sanger:assay:4245047:1	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	01/11/07	01/16/07	127	NA	unknown
ss70700778	ILLUMINA\|HumanHap550v3.0__rs2073478	rev/T	A/C	actcgatcccgctccactaggtctgccagg	ggttcagcagccggccccgctcagaggcat	04/20/07	03/30/08	130	Genomic	unknown
ss71266837	ILLUMINA\|HumanHap650Yv3.0_rs2073478	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	04/23/07	04/23/07	127	Genomic	unknown
ss75503425	ILLUMINA\|ILMN_Human_1M_rs2073478	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	08/28/07	08/29/07	129	Genomic	unknown
ss76547315	AFFY\|AFFY_6_1M_SNP_A-8408582	fwd/B	G/T	ggccggctgctgaacc	cctggcagacctagtg	08/28/07	08/30/07	130	Genomic	unknown
ss76892366	SI_EXO\|NT_008413.17_38386065	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	09/20/07	09/20/07	129	Genomic	unknown
ss79112639	ILLUMINA\|HumanHap300v2.0_rs2073478	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	04/18/07	11/18/07	130	Genomic	unknown
ss83965869	KRIBB_YJKIM\|KHS586581	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	12/04/07	12/06/07	130	Genomic	unknown
ss84160481	PHARMGKB_AB_DME\|PS206163_PA149405537_301	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	12/06/07	12/10/07	130	Genomic	unknown
ss86344124	CANCER-GENOME\|14225	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	01/25/08	01/25/08	129	Genomic	unknown
ss94051083	BCMHGSC_JDW\|JWB-2590451	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	02/26/08	03/05/08	129	Genomic	unknown
ss97723108	HUMANGENOME_JCVI\|1103652078189	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	03/30/08	03/30/08	130	Genomic	unknown
ss105437824	SNP500CANCER\|ALDH1B1-03	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	09/05/08	09/05/08	130	Genomic	unknown
ss108769552	1000GENOMES\|CEU.trio.12.15.2008_2177094_chr9_38386065	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	12/15/08	12/16/08	130	Genomic	unknown
ss114480217	1000GENOMES\|NA19240_2008_12_16_1967529_chr9_38386065	fwd/B	G/T	atgcctctgagcggggccggctgctgaacc	cctggcagacctagtggagcgggatcgagt	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 CTGGTGGGCC CTTGGGTACC GCCACCTGCC TTCTCCCACC TGTTCACCCT GGTTTCTTTT
 GTCCCTCTCC AGAGTGTCAG CATGCTGCGC TTCCTGGCAC CCCGGCTGCT TAGCCTCCAG
 GGCAGGACCG CCCGCTACTC CTCGGCAGCA GCCCTCCCAA GCCCCATTCT GAACCCAGAC
 ATCCCCTACA ACCAGCTGTT CATCAACAAT GAATGGCAAG ATGCAGTCAG CAAGAAGACC
 TTCCCGACGG TCAACCCTAC CACCGGGGAG GTCATTGGGC ACGTGGCTGA AGGTGACCGG
 GCTGATGTGG ATCGGGCCGT GAAAGCAGCC CGGGAAGCCT TCCGCCTGGG GTCCCCATGG
 CGCCGGATGG ATGCCTCTGA GCGGGGCCGG CTGCTGAACC
 K
 CCTGGCAGAC CTAGTGGAGC GGGATCGAGT CTACTTGGCC TCACTCGAGA CCTTGGACAA
 TGGGAAGCCT TTCCAAGAGT CTTACGCCTT GGACTTGGAT GAGGTCATCA AGGTGTATCG
 GTACTTTGCT GGCTGGGCTG ACAAGTGGCA TGGCAAGACC ATCCCCATGG ATGGCCAGCA
 TTTCTGCTTC ACCCGGCATG AGCCCGTTGG TGTCTGTGGC CAGATCATCC CGTGGAACTT
 CCCCTTGGTC ATGCAGGGTT GGAAACTTGC CCCGGCACTC GCCACAGGCA ACACTGTGGT
 TATGAAGGTG GCAGAGCAGA CCCCCCTCTC TGCCCTGTAT TTGGCCTCCC TCATCAAGGA
 GGCAGGCTTT CCCCCTGGGG TGGTGAACAT CATCACGGGG

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_008413.17 ABBA01050381 BC001619 BM458404

dbSNP Blast Analysis

UniGene Cluster ID
436219

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	G/G	G/T	T/T	HWP	A	C	G	T
ss105437824	P1		194	GF				0.309	0.464	0.227				0.541	0.459

	CAUC1		56	GF				0.179	0.500	0.321				0.429	0.571

	AFR1		46	GF				0.435	0.391	0.174				0.630	0.370

	HISP1		44	GF				0.227	0.545	0.227				0.500	0.500

	PAC1		48	GF				0.417	0.417	0.167				0.625	0.375

	P2		418	GF				0.416	0.392	0.191				0.612	0.388

	CAUC2		120	GF				0.200	0.450	0.350				0.425	0.575

	AFR2		120	GF				0.600	0.317	0.083				0.758	0.242

	ASI2		178	GF				0.438	0.404	0.157				0.640	0.360

ss19799525	CEPH		184	AF										0.370	0.630

	EURAME		32	GF				0.438	0.312	0.250	0.200			0.594	0.406

	AFRAME		32	GF				0.125	0.438	0.438	1.000			0.344	0.656

ss23587937	AFD_EUR_PANEL	European	48	IG				0.167	0.500	0.333	1.000			0.417	0.583

	AFD_AFR_PANEL	African American	40	IG				0.200	0.500	0.300	1.000			0.450	0.550

	AFD_CHN_PANEL	Asian	42	IG				0.524	0.429	0.048	0.655			0.738	0.262

ss2987805	JBIC-allele		1296	AF										0.669	0.331

ss3172732	WIAF-CSNP-MITOGPOP5	multiple	36	IG				0.389	0.278	0.333	0.100			0.528	0.472

ss48430137	HapMap-CEU	European	120	IG				0.200	0.417	0.383	0.403			0.408	0.592

	HapMap-HCB	Asian	90	IG				0.511	0.333	0.156	0.150			0.678	0.322

	HapMap-JPT	Asian	88	IG				0.364	0.500	0.136	0.752			0.614	0.386

	HapMap-YRI	Sub-Saharan African	116	IG				0.603	0.310	0.086	0.251			0.759	0.241

	AGI_ASP population	multiple	78	IG	0.282	0.410	0.308				0.273	0.487	0.513

ss84160481	PA149405538		350	AF										0.600	0.400

Concordant Genotype	Total Sample	A/A	A/C	C/C	G/G	G/T	T/T
ss23587937	71				19	31	15
ss3172732	15				5	5	5
ss48430137	37	11	15	11
ss76892366	1206				472	504	201
ss97723108	1						1

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C	G/G	G/T	T/T
rs2073478	1316	11	15	11	493	534	218

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
536	ss3172732	G/G	WIAF-CSNP	WIAF-CSNP-MITOGPOP5	CL8		06.18.01-a
536	ss76892366	T/T	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch9_CEU_affymetrix:genomewidesnp_6.0
1696	ss3172732	G/G	WIAF-CSNP	WIAF-CSNP-MITOGPOP5	CL78		06.18.01-a
1696	ss48430137	C/C	APPLERA_GI	AGI_ASP population	NA14663		3-1
1697	ss3172732	T/T	WIAF-CSNP	WIAF-CSNP-MITOGPOP5	CL79		06.18.01-a
1697	ss48430137	A/C	APPLERA_GI	AGI_ASP population	NA14665		3-1

Genotype data submitted for	1336	samples from	1316	individuals	Individual with multiple genotypes submission:	20

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

YES

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Revised: May 25, 2006 1:38 PM .