Reference SNP(refSNP) Cluster Report: rs2180314

Reference SNP(refSNP) Cluster Report: rs2180314

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:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_000846.3:c.335C>G
NP_000837.2:p.Thr112Ser

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3117044 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2180314 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
ss3117044	TSC-CSHL\|TSC1223530	fwd/B	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	06/07/01	04/07/04	96	Genomic	unknown
ss4395060	LEE\|ge466532	rev/T	C/G	tgggtgaaatgatccttcttctgcccttta	tcaacctgaggaacaagatgccaagcttgc	04/25/02	10/10/03	106	cDNA	unknown
ss12797143	SC_SNP\|NT_007592.13_43414839	fwd/B	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	10/21/03	11/17/03	119	Genomic	unknown
ss16266078	CGAP-GAI\|1532556	rev/T	C/G	tgggtgaaatgatccttcttctgcccttta	tcaacctgaggaacaagatgccaagcttgc	11/18/03	11/22/03	120	cDNA	unknown
ss22475696	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007592.13_43414839	fwd/B	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	03/21/04	03/21/04	121	Genomic	unknown
ss24377624	PERLEGEN\|afd4064850	fwd/B	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	08/10/04	09/13/04	124	Genomic	unknown
ss28503984	MGC_GENOME_DIFF\|BC002895x29804415-C43414839G	fwd/B	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	08/25/04	08/25/04	126	cDNA	unknown
ss65726320	ILLUMINA\|Human1-rs2180314	fwd/B	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	10/10/06	10/10/06	127	Genomic	unknown
ss68412188	CSHL-HAPMAP\|sanger:assay:395523:1	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	01/11/07	01/16/07	127	NA	unknown
ss74813355	AFFY\|SNP_M-289429	fwd/B	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	08/09/07	08/09/07	128	Genomic	unknown
ss74890660	ILLUMINA\|ILMN_Human_1M_rs2180314	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	08/28/07	08/29/07	129	Genomic	unknown
ss81747148	HGSV\|Cor18956_SNV_20070510.chr6_52725690	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	11/30/07	12/01/07	130	Genomic	unknown
ss84168937	PHARMGKB_AB_DME\|PS206042_PA147533381_301	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	12/06/07	12/09/07	130	Genomic	unknown
ss86241758	CORNELL\|hCV22275149	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	01/21/08	01/21/08	129	Genomic	unknown
ss93461034	BCMHGSC_JDW\|JWB-2140445	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	02/26/08	03/04/08	129	Genomic	unknown
ss98393603	HUMANGENOME_JCVI\|1103652868547	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	03/31/08	03/31/08	130	Genomic	unknown
ss104313396	BGI\|BGI_rs2180314	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	06/08/08	06/19/09	130	Genomic	unknown
ss105440013	SNP500CANCER\|GSTA2-06	rev/	C/G	tgggtgaaatgatccttcttctgyccttta	tcaacctgaggaacaagatgccaagcttgc	09/05/08	09/05/08	130	Genomic	unknown
ss110127085	1000GENOMES\|CEU.trio.12.15.2008_1520900_chr6_52725690	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	12/15/08	12/17/08	130	Genomic	unknown
ss114370610	1000GENOMES\|NA19240_2008_12_16_1363726_chr6_52725690	fwd/	C/G	gcaagcttggcatcttgttcctcaggttga	taaagggcagaagaaggatcatttcaccca	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 GCATTTTACA GAATCTTCCT CTGCATCCCA CAGTCACTCT CCTTTTAAAA AATACTGATC
 CCTGAAACAC TGCAATATTC TCTGGTTGGG CAATTGGTCT CCTGTCTTCC TGCATATGGT
 GCCAGAATGT TTTCTGATGG ATCACTTTCA TCATGCCCCT GTTCAAAGTC CATGGGGTTC
 CATAGACTGA ACAGCAACTC TAGTGTGGTC CAGAGCCTTC CACAGCCCAC ATTCTACTTA
 TGAACACAAA ATTCTGTTGA ACAGATAATT CCATATTGGG GTTCAGTAAA TTAAAATTTT
 ACTGGAAGAT TATAGCTTGG GTATAAGTGA TACAATTGTT TCTCCAAGTC TATTTTCATA
 AAATGCCTTG AGAGTCAGAG TGCTGCATTG GTGTCCAGGA AGTATCACTG AAAGTGAAGA
 TCAGTGCCCC AGGAATGCCC AGCCACTATT TTTCTACTGG CTTCTAAACT CAGTTCCCCA
 AAACACTGAA CAGCTTCACT TACTTTTTCA AAGGCAGGGA AGTAGCGATT TTTTGTTTTC
 TCTTGGATCA AGGCAAGCTT GGCATCTTGT TCCTCAGGTT GA
 S
 TAAAGGGCAG AAGAAGGATC ATTTCACCCA AATCTGCTAT ACCTTCTATA TAC

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_007592 ABBA01050548 BC002895 BE796134 Hs.89552

dbSNP Blast Analysis

UniGene Cluster ID
94107

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss105440013	P1		200	GF	0.260	0.420	0.320		0.470	0.530

	CAUC1		60	GF	0.133	0.567	0.300		0.417	0.583

	AFR1		48	GF	0.583	0.333	0.083		0.750	0.250

	HISP1		44	GF	0.227	0.182	0.591		0.318	0.682

	PAC1		48	GF	0.125	0.542	0.333		0.396	0.604

	P2		420	GF	0.290	0.410	0.300		0.495	0.505

	CAUC2		120	GF	0.183	0.500	0.317		0.433	0.567

	AFR2		120	GF	0.583	0.383	0.033		0.775	0.225

	P3		552	GF	0.221	0.409	0.370		0.426	0.574

	CAUC3		132	GF	0.136	0.530	0.333		0.402	0.598

	AFR3		150	GF	0.547	0.387	0.067		0.740	0.260

	HISP3		96	GF		0.042	0.958		0.021	0.979

	PAC3		174	GF	0.126	0.540	0.333		0.397	0.603

	ASI2		180	GF	0.167	0.367	0.467		0.350	0.650

ss24377624	AFD_EUR_PANEL	European	48	IG	0.125	0.542	0.333	0.527	0.396	0.604

	AFD_AFR_PANEL	African American	44	IG	0.500	0.273	0.227	0.100	0.636	0.364

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.375	0.542	1.000	0.271	0.729

ss3117044	SC_12_A	Asian	24	IG	0.083	0.500	0.417	0.752	0.333	0.667

	SC_12_AA	African American	22	IG	0.636	0.273	0.091	0.479	0.773	0.227

	SC_12_C	European	14	IG	0.286	0.286	0.429	0.273	0.429	0.571

	SC_95_C	European	92	IG	0.283	0.304	0.413	0.010	0.435	0.565

	HapMap-CEU	European	114	IG	0.158	0.544	0.298	0.439	0.430	0.570

	HapMap-HCB	Asian	90	IG	0.111	0.378	0.511	0.527	0.300	0.700

	HapMap-JPT	Asian	88	IG	0.205	0.341	0.455	0.100	0.375	0.625

	HapMap-YRI	Sub-Saharan African	118	IG	0.576	0.390	0.034	0.527	0.771	0.229

ss84168937	PA147533382		354	AF					0.444	0.556

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss24377624	71	16	28	26
ss3117044	612	101	142	97
ss98393603	1			1

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs2180314	646	112	163	121

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
229	ss3117044	G/G	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss3117044	N/N	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229	ss3117044	C/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r27_ch6_CEU_illumina:golden_gate_1.0.0
231	ss3117044	C/C	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
231	ss3117044	G/G	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE

Genotype data submitted for	728	samples from	646	individuals	Individual with multiple genotypes submission:	72

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 .