Reference SNP(refSNP) Cluster Report: rs2270941

Reference SNP(refSNP) Cluster Report: rs2270941

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:	T
Clinical Association:	unknown

HGVS Names
NM_014475.3:c.197G>A
NP_055290.1:p.Ser66Asn
NT_011109.15:g.21706553G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76890834 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2270941 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
ss3205549	YUSUKE\|IMS-JST065633	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	09/05/01	10/10/03	100	Genomic	unknown
ss6903783	SNP500CANCER\|DHDH-01	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	02/14/03	04/07/04	116	Genomic	unknown
ss20063625	CSHL-HAPMAP\|CSHL-HuFF-200402.chr19.NT_011109.15_21706553	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	02/21/04	03/04/04	120	Genomic	unknown
ss24225624	PERLEGEN\|afd1615172	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	08/10/04	09/13/04	123	Genomic	unknown
ss44164897	ABI\|hCV3170900	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	07/18/05	11/03/06	126	Genomic	unknown
ss48404982	APPLERA_GI\|hCV3170900	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	09/28/05	11/03/06	126	Genomic	unknown
ss65726407	ILLUMINA\|Human1-rs2270941	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	10/10/06	10/10/06	127	Genomic	unknown
ss66676979	ILLUMINA\|HumanHap300v1.1_rs2270941	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	11/09/06	11/09/06	127	Genomic	unknown
ss67239833	ILLUMINA\|HumanHap550v1.1_rs2270941	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	11/14/06	11/14/06	127	Genomic	unknown
ss67636423	ILLUMINA\|HumanHap650Yv1.0_rs2270941	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	11/14/06	11/14/06	127	Genomic	unknown
ss69229884	PERLEGEN\|PGP01615172	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	01/30/07	08/14/07	127	Genomic	unknown
ss70718172	ILLUMINA\|HumanHap550v3.0__rs2270941	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	04/20/07	03/30/08	130	Genomic	unknown
ss71286343	ILLUMINA\|HumanHap650Yv3.0_rs2270941	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	04/23/07	04/23/07	127	Genomic	unknown
ss74806253	AFFY\|SNP_M-175343	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	08/09/07	08/09/07	128	Genomic	unknown
ss75555358	ILLUMINA\|ILMN_Human_1M_rs2270941	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	08/28/07	08/29/07	129	Genomic	unknown
ss76890834	SI_EXO\|NT_011109.15_21706553	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	09/20/07	09/20/07	129	Genomic	unknown
ss79124773	ILLUMINA\|HumanHap300v2.0_rs2270941	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	04/18/07	11/18/07	130	Genomic	unknown
ss79908868	HGSV\|Cor18507_SNV_20070510.chr19_54130175	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	11/23/07	11/24/07	130	Genomic	unknown
ss84014448	KRIBB_YJKIM\|KHS602155	fwd/B	C/T	cacccccatcgccctcgccactcacccacg	tcgggtccttggccagctcctcataggagc	12/04/07	12/06/07	130	Genomic	unknown
ss85405539	HGSV\|Cor19129_SNV_20070510.chr19_54130175	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	12/06/07	12/09/07	130	Genomic	unknown
ss115225002	1000GENOMES\|NA19240_2008_12_16_3270750_chr19_54130175	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	12/18/08	12/19/08	130	Genomic	unknown
ss117725824	ILLUMINA-UK\|NA18507_000055286_NCBI36.1_chr19_54130175	rev/T	A/G	gctcctatgaggagctggccaaggacccga	cgtgggtgagtggcgagggcgatgggggtg	01/19/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 CTCTGTCGCC CAGGCTGGAG TGCAGTGGCG CGATCTTGGC TCACTTCAAC CTCTGCTTCC
 CGGATTCAAG TGATTCTCCT GCCTCAGCCT CCCCAGTAGC TGGGATTACA GGTGCGTGCC
 ACCATACCTG GCTAATTTAT TTTTATTGTT ATTTTTTGTA GAGATTGGGT CTTGCTACGT
 TGCCGAGGCT GGTCTCGAAC GCTAAGTGTA GTTTAACACC TACTAGACAG CCAGTCCCAG
 ACCAAGCCCG TTTTATAGTT CTCCTCCCAG CCAAAGGTCT TTATGGAACC CAAAGGGATT
 GGACCATCCT GAGGAGCCTT GCATCTCCCA GGGGGCAGCC AGGGGGCACC GCTCCAGGGG
 CGGCGGCCAG CACCCCCATC GCCCTCGCCA CTCACCCACG
 Y
 TCGGGTCCTT GGCCAGCTCC TCATAGGAGC CGTAGGCCTT GGGGATGTCG TGTTTCTGTG
 CAAACTCCTT CGCACGGCTC AGATCGCGGG CCGCCACCGC CACCACCTGG AGGGGCACAA
 GAATCGGATT TGAGGGGCTG AGGCAGGCGT GGAAACTGGG TGGAAGGGAG GCAAAGGAGG
 AGGCTCTGGC CAGGGGAAGG GGAGACGTGG TCCTGGGGGA AGAGATGACG GGGGCTGGAC
 ATTTGGGCCC TGGGAAAGAG AGATCTGGGG GAAAGCCGTT ATTAAATCCC CCAATATTGA
 AATTATCTTC ATAGTAGCTT ACATCAAGGC CTTTCCAAAC CTCAAGACAC TCAGGTTTGT
 GTGGGGAAAA GAAAGAGAGA TCAGATTGTT ACTGTGTCTA

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_011109.15

dbSNP Blast Analysis

UniGene Cluster ID
405755

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24225624	AFD_EUR_PANEL	European	48	IG	0.542	0.375	0.083	1.000	0.729	0.271

	AFD_AFR_PANEL	African American	44	IG	0.045	0.409	0.545	0.752	0.250	0.750

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.542	0.333	0.527	0.396	0.604

ss3205549	JBIC-allele		1488	AF					0.455	0.545

ss44164897	HapMap-CEU	European	120	IG	0.617	0.333	0.050	1.000	0.783	0.217

	HapMap-HCB	Asian	90	IG	0.133	0.511	0.356	0.655	0.389	0.611

	HapMap-JPT	Asian	88	IG	0.205	0.614	0.182	0.150	0.511	0.489

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.433	0.550	0.150	0.233	0.767

	AoD_African_American		90	AF					0.350	0.650

	AoD_Caucasian		92	AF					0.750	0.250

ss48404982	AGI_ASP population	multiple	76	IG	0.368	0.289	0.342	0.010	0.513	0.487

ss6903783	P1		198	GF	0.303	0.394	0.303	0.050	0.500	0.500

	CAUC1		56	GF	0.500	0.393	0.107	0.752	0.697	0.303

	AFR1		48	GF		0.250	0.750	0.527	0.125	0.875

	HISP1		46	GF	0.348	0.435	0.217	0.584	0.565	0.435

	PAC1		48	GF	0.333	0.500	0.167	1.000	0.583	0.417

ss69229884	HapMap-CEU	European	120	GF	0.650	0.317	0.033		0.808	0.192

	HapMap-HCB	Asian	90	GF	0.133	0.533	0.333		0.400	0.600

	HapMap-JPT	Asian	90	GF	0.200	0.644	0.156		0.522	0.478

	HapMap-YRI	Sub-Saharan African	120	GF	0.033	0.467	0.500		0.267	0.733

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24225624	70
ss48404982	38
ss76890834	1195

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2270941	1301

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
170	ss76890834	A/A	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	r27_ch19_CEU_illumina:human_1m_beadchip
213	ss76890834	A/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	r27_ch19_CEU_illumina:human_1m_beadchip
348	ss24225624	A/A	PERLEGEN	AFD_EUR_PANEL	NA10860		71_IND_CHR_19
348	ss76890834	N/N	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r27_ch19_CEU_illumina:human_1m_beadchip
5140	ss76890834	A/A	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	r27_ch19_YRI_illumina:human_1m_beadchip
5165	ss76890834	A/A	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r27_ch19_CHB_illumina:human_1m_beadchip
5215	ss76890834	A/A	CSHL-HAPMAP	HapMap-JPT	NA18975	JA18975	r27_ch19_JPT_illumina:human_1m_beadchip
5240	ss76890834	A/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r27_ch19_YRI_illumina:human_1m_beadchip
5241	ss76890834	A/A	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r27_ch19_YRI_illumina:human_1m_beadchip
5256	ss76890834	A/A	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	r27_ch19_YRI_illumina:human_1m_beadchip
5272	ss76890834	A/A	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	r27_ch19_YRI_illumina:human_1m_beadchip
5294	ss76890834	A/A	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r27_ch19_YRI_illumina:human_1m_beadchip
5307	ss76890834	N/N	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r27_ch19_YRI_illumina:human_1m_beadchip

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

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .