Reference SNP(refSNP) Cluster Report: rs2245203

Reference SNP(refSNP) Cluster Report: rs2245203

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/130
Map to Genome Build:	36.3

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

HGVS Names
NM_033045.3:c.616A>G
NP_149034.2:p.Ile206Val
NT_029419.11:g.14920819T>C
XM_001718424.1:c.1357+3124G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48416258 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2245203 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
ss3205767	YUSUKE\|IMS-JST065851	fwd/B	C/T	tctcgaagagtggctccaggttgctcctga	acatttctgctcttggaggaagctccactt	09/05/01	10/10/03	100	Genomic	unknown
ss4038698	SC_JCM\|AP002519.2_6211	rev/T	A/G	aagtggaacttcctccaagagcagaaatgt	tcaggagcaacctggagccactcttcgaga	09/26/01	10/10/03	100	Genomic	unknown
ss23356304	PERLEGEN\|afd2039792	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	08/10/04	09/13/04	123	Genomic	unknown
ss48416258	APPLERA_GI\|hCV15959428	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	09/28/05	11/03/06	126	Genomic	unknown
ss66556460	ILLUMINA\|HumanHap300v1.1_rs2245203	fwd/B	C/T	tctcgaagagtggctccaggttgctcctga	acatttctgctcttggaggaagttccactt	11/09/06	11/09/06	127	Genomic	unknown
ss67237415	ILLUMINA\|HumanHap550v1.1_rs2245203	fwd/B	C/T	tctcgaagagtggctccaggttgctcctga	acatttctgctcttggaggaagttccactt	11/14/06	11/14/06	127	Genomic	unknown
ss67633718	ILLUMINA\|HumanHap650Yv1.0_rs2245203	fwd/B	C/T	tctcgaagagtggctccaggttgctcctga	acatttctgctcttggaggaagttccactt	11/14/06	11/14/06	127	Genomic	unknown
ss69109164	PERLEGEN\|PGP02039792	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	01/30/07	08/14/07	127	Genomic	unknown
ss70715739	ILLUMINA\|HumanHap550v3.0__rs2245203	rev/T	A/G	aagtggagcttcctccaagagcagaaatgt	tcaggagcaatctggagccactcttcgaga	04/20/07	03/30/08	130	Genomic	unknown
ss71283623	ILLUMINA\|HumanHap650Yv3.0_rs2245203	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	04/23/07	04/23/07	127	Genomic	unknown
ss75681172	ILLUMINA\|ILMN_Human_1M_rs2245203	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	08/28/07	08/29/07	129	Genomic	unknown
ss79123083	ILLUMINA\|HumanHap300v2.0_rs2245203	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	04/18/07	11/18/07	130	Genomic	unknown
ss80641391	HGSV\|Cor18507_SNV_20070510.chr12_51063780	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	11/23/07	11/26/07	130	Genomic	unknown
ss85154233	HGSV\|Cor19240_SNV_20070510.chr12_51063780	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	11/30/07	12/08/07	130	Genomic	unknown
ss111944609	1000GENOMES\|CEU.trio.12.15.2008_2736702_chr12_51063780	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	12/15/08	12/17/08	130	Genomic	unknown
ss113546856	1000GENOMES\|NA19240_2008_12_16_2459921_chr12_51063780	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	12/18/08	12/18/08	130	Genomic	unknown
ss118808084	ILLUMINA-UK\|NA18507_000067174_NCBI36.1_chr12_51063780	fwd/B	C/T	tctcgaagagtggctccagattgctcctga	acatttctgctcttggaggaagctccactt	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 TTCTCTGTTC ACATATCTCT ACCCACCCCC ACCTCCCCAG GCTTGATGTG GTAACCAGCA
 TTCAACCCTG ATCCTTCCAG CTGCTCTCAT CTGAGCTTGG CAGCTAATTC TGGGGCCAGG
 CCTGGCCTGT CACTGGTCTG TGCAGCTCAG ATGTCACTCA CTTCTTCTTG AAGCCCTCTA
 GGACATCCTG CAGGTGGTTC CTCTCAGCCT GGAGCCGGGC CTGATCACTG ACCAGCACCT
 CCAACTGCCT CCGCAGGTTG GTGATGTAGC TCTCGAAGAG TGGCTCCAGA TTGCTCCTGA
 Y
 ACATTTCTGC TCTTGGAGGA AGCTCCACTT GGTCTCTAGG AGCTTATTCT GCTGCTCTAG
 GAACCGAACC TAAATCCACA GGGCACAGAA ATGGCATTTG AAGTGCTTGA TAGGGTTCAT
 GCCTTGACCA AGCTCTTGAG ATGGCCAGCG ATGACTTGAC CACATGTCGA CAGGGTTCTC
 TCCTCTGCTG ACTTTCATTC CTCCACTAAC TCAGCAGAAG CTGGAAGGGC AGGTTGTGAC
 TCCCTCCTTG TGCTCGGCTA GGCCTAGTTA CCAATATGGG GTTTTGAACC ATAGCACTTC

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
NC_000012.9 AC027562

dbSNP Blast Analysis

UniGene Cluster ID
272336

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23356304	AFD_EUR_PANEL	European	48	IG	0.083	0.417	0.500	1.000	0.292	0.708

	AFD_AFR_PANEL	African American	46	IG	0.217	0.609	0.174	0.294	0.522	0.478

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.208	0.708	0.150	0.188	0.812

ss48416258	HapMap-CEU	European	114	IG	0.053	0.351	0.596		0.228	0.772

	HapMap-HCB	Asian	90	IG	0.044	0.378	0.578	0.584	0.233	0.767

	HapMap-JPT	Asian	90	IG	0.067	0.333	0.600	0.752	0.233	0.767

	HapMap-YRI	Sub-Saharan African	112	IG	0.357	0.482	0.161	0.527	0.598	0.402

	AGI_ASP population	multiple	66	IG	0.273	0.303	0.424	0.050	0.424	0.576

ss69109164	HapMap-CEU	European	118	GF	0.068	0.288	0.644		0.212	0.788

	HapMap-HCB	Asian	90	GF	0.044	0.556	0.400		0.322	0.678

	HapMap-JPT	Asian	90	GF	0.044	0.444	0.511		0.267	0.733

	HapMap-YRI	Sub-Saharan African	120	GF	0.333	0.500	0.167		0.583	0.417

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss23356304	70	8	29	33
ss48416258	1219	185	455	550

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2245203	1301	193	480	576

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
169	ss48416258	T/T	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	r27_ch12_CEU_illumina:human_1m_beadchip	4776157
188	ss23356304	C/C	PERLEGEN	AFD_EUR_PANEL	NA10851		71_IND_CHR_12
188	ss48416258	N/N	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r27_ch12_CEU_illumina:human_1m_beadchip	4776157
200	ss48416258	C/T	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r27_ch12_CEU_illumina:human_1m_beadchip	4776157
255	ss48416258	T/T	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r27_ch12_CEU_illumina:human_1m_beadchip	4776157
262	ss48416258	C/T	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r27_ch12_CEU_illumina:human_1m_beadchip	4776157
535	ss48416258	C/T	CSHL-HAPMAP	HapMap-CEU	NA12750	CEPH1444.13	r27_ch12_CEU_illumina:human_1m_beadchip	4776157
5141	ss48416258	C/C	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	r27_ch12_YRI_illumina:human_1m_beadchip	4776157
5158	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18605	CH18605	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5161	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5163	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18609	CH18609	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5171	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18563	CH18563	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5173	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18612	CH18612	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5187	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5188	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18635	CH18635	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5190	ss48416258	T/T	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	r27_ch12_CHB_illumina:human_1m_beadchip	4776157
5208	ss48416258	T/T	CSHL-HAPMAP	HapMap-JPT	NA18969	JA18969	r27_ch12_JPT_illumina:human_1m_beadchip	4776157
5212	ss48416258	T/T	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	r27_ch12_JPT_illumina:human_1m_beadchip	4776157
5215	ss48416258	T/T	CSHL-HAPMAP	HapMap-JPT	NA18975	JA18975	r27_ch12_JPT_illumina:human_1m_beadchip	4776157
5226	ss48416258	T/T	CSHL-HAPMAP	HapMap-JPT	NA18990	JA18990	r27_ch12_JPT_illumina:human_1m_beadchip	4776157
5227	ss48416258	C/C	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	r27_ch12_JPT_illumina:human_1m_beadchip	4776157
5247	ss48416258	C/C	CSHL-HAPMAP	HapMap-YRI	NA18515	YOR013.01	r27_ch12_YRI_illumina:human_1m_beadchip	4776157
5251	ss48416258	N/N	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	r27_ch12_YRI_illumina:human_1m_beadchip	4776157
5259	ss48416258	C/C	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r27_ch12_YRI_illumina:human_1m_beadchip	4776157
5260	ss48416258	C/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r27_ch12_YRI_illumina:human_1m_beadchip	4776157
5277	ss48416258	T/T	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r27_ch12_YRI_illumina:human_1m_beadchip	4776157
5299	ss48416258	C/T	CSHL-HAPMAP	HapMap-YRI	NA19116	YOR060.02	r27_ch12_YRI_illumina:human_1m_beadchip	4776157

Genotype data submitted for	1316	samples from	1301	individuals	Individual with multiple genotypes submission:	15

Validation Summary:

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .