Reference SNP(refSNP) Cluster Report: rs887241

Reference SNP(refSNP) Cluster Report: rs887241

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
Map to Genome Build:	36.3

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

HGVS Names
NM_000691.3:c.400T>G
NM_000691.4:c.400T>G
NM_001135167.1:c.400T>G
NM_001135168.1:c.400T>G
NP_000682.3:p.Ser134Ala
NP_001128639.1:p.Ser134Ala
NP_001128640.1:p.Ser134Ala
NT_010718.15:g.19243154A>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1315276 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs887241 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
ss1315276	TSC-CSHL\|TSC0155475	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	09/06/00	04/07/04	86	Genomic	95 %
ss1509145	LEE\|8080	fwd/B	G/T	cccatggtgggcgccatcgctgcagggaac	cagtggtcctcaagccctcggagctgagtg	09/13/00	10/10/03	102	cDNA	unknown
ss6312394	RIKENSNPRC\|ssj0008064	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	01/15/03	10/10/03	111	Genomic	unknown
ss12412060	WI_SSAHASNP\|chr17.NT_030843.6_506224	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	07/04/03	10/10/03	116	Genomic	unknown
ss13612152	WI_SSAHASNP\|chr17.NT_030843.7_506224	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	11/05/03	11/22/03	119	Genomic	unknown
ss14300234	BCM_SSAHASNP\|chr17.NT_030843.7_506224	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	11/05/03	11/22/03	119	Genomic	unknown
ss21418789	SSAHASNP\|WGSA-200403-chr17.chr17.NT_030843.7_506224	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	03/19/04	03/20/04	121	Genomic	unknown
ss24596928	PERLEGEN\|afd0815449	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	08/10/04	09/13/04	123	Genomic	unknown
ss28510414	MGC_GENOME_DIFF\|BC004370x37544716-A506224C	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	08/25/04	08/25/04	126	cDNA	unknown
ss28510581	MGC_GENOME_DIFF\|BC008892x37544716-A506224C	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	08/25/04	08/25/04	126	cDNA	unknown
ss28510937	MGC_GENOME_DIFF\|BC021194x37544716-A506224C	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	08/25/04	08/25/04	126	cDNA	unknown
ss44042833	ABI\|hCV7443700	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	07/18/05	11/03/06	126	Genomic	unknown
ss65732103	ILLUMINA\|Human1-rs887241	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	10/10/06	10/10/06	127	Genomic	unknown
ss66286489	AFFY\|SNP_A-1811549	fwd/B	G/T	gtgctctgcagggaac	cagtggtcctcaagcc	10/29/06	08/14/07	127	Genomic	unknown
ss66547728	ILLUMINA\|HumanHap300v1.1_rs887241	fwd/T	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	11/09/06	11/09/06	127	Genomic	unknown
ss67887924	ILLUMINA\|HumanHap550v1.1_rs887241	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	11/14/06	11/14/06	127	Genomic	unknown
ss68025847	ILLUMINA\|HumanHap650Yv1.0_rs887241	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	11/14/06	11/15/06	127	Genomic	unknown
ss69193632	PERLEGEN\|PGP00815449	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	01/30/07	08/14/07	127	Genomic	unknown
ss70978605	ILLUMINA\|HumanHap550v3.0__rs887241	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	04/20/07	03/31/08	130	Genomic	unknown
ss71590485	ILLUMINA\|HumanHap650Yv3.0_rs887241	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	04/23/07	04/23/07	127	Genomic	unknown
ss75744303	ILLUMINA\|ILMN_Human_1M_rs887241	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	08/28/07	08/29/07	129	Genomic	unknown
ss75947635	AFFY\|AFFY_6_1M_SNP_A-1811549	fwd/B	G/T	gtgctctgcagggaac	cagtggtcctcaagcc	08/28/07	08/29/07	129	Genomic	unknown
ss79286854	ILLUMINA\|HumanHap300v2.0_rs887241	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	04/18/07	11/18/07	130	Genomic	unknown
ss81971984	HGSV\|Cor18555_SNV_20070510.chr17_19586530	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	11/27/07	12/01/07	130	Genomic	unknown
ss82551623	HGSV\|Cor19240_SNV_20070510.chr17_19586530	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	11/30/07	12/03/07	130	Genomic	unknown
ss83595215	KRIBB_YJKIM\|KHS497997	fwd/B	G/T	aggcctggctcggtgtgctctgcagggaac	cagtggtcctcaagccctcggagctgagtg	12/04/07	12/05/07	130	Genomic	unknown
ss86271445	CORNELL\|hCV7443700	rev/B	G/T	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	01/21/08	01/21/08	129	Genomic	unknown
ss86344496	CANCER-GENOME\|12660	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	01/25/08	01/25/08	129	Genomic	unknown
ss96540036	HUMANGENOME_JCVI\|1103645295752	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	03/26/08	03/26/08	130	Genomic	unknown
ss106501689	BGI\|BGI_rs887241	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	09/15/08	06/18/09	130	Genomic	unknown
ss109692494	1000GENOMES\|CEU.trio.12.15.2008_3381195_chr17_19586530	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	12/15/08	12/16/08	130	Genomic	unknown
ss113382979	1000GENOMES\|NA19240_2008_12_16_3039112_chr17_19586530	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	12/18/08	12/18/08	130	Genomic	unknown
ss118020278	ILLUMINA-UK\|NA18507_000025769_NCBI36.1_chr17_19586530	rev/T	A/C	cactcagctccgagggcttgaggaccactg	gttccctgcagagcacaccgagccaggcct	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 ACAGAGAGGG CCTGCCTTCC CCCACCCCTG TTGGGGGGCT GGAGCTTCTG TCACCTAATA
 TGCATCAGGG CTTCCTTCCT AGAATGGGCC AGCGCTGTTC TACCAACCGG GCCCCCAGAG
 CCTCTCTCCC CTTTCTGCTT TTCCTCCAAC ATCTCAGCAA CTCAGAGGGC CAGGTGGTGC
 AGCTCTGGCC AGCGTGTGCC CGTGTGTGTC CCTCTGTCAT GTGCCCGTGC GTGCTCCTGG
 GTGTGCCCCG TGACATGTGC TTGTTTGCTA ACAACTCTTC CATCCACTGT CCCGAGGACA
 CACAATGGAG GGGAGGCTTC AGGTGTGGTC CTTGGGAGGG CAGAGCCTCT GGTGAAGTAC
 CCTGGGCATA GGCCTGGCTC GGTGTGCTCT GCAGGGAAC
 K
 CAGTGGTCCT CAAGCCCTCG GAGCTGAGTG AGAACATGGC GAGCCTGCTG GCTACCATCA
 TCCCCCAGTA CCTGGACAAG GTGAGTTGCC CTCCAGGGCC TCGTAACTCC ATGGCCTCAT
 AACTGAGCTA GGGCCAGGTC TTTGGGGGGT GAGAAATAGT GAATTCTTGC AGCAAGGGGC
 CAAGCTACTG GTGGGGCTGA GGATTGTTCT TAGC

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_030843 ABBA01054596 AC005722.1 BC004370 BC008892 BC021194 Hs.575

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail						Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G	G/G	G/T	T	T/T	HWP	G	T
ss1315276	SC_12_A	Asian	24	IG		0.750	0.250			0.655	0.875	0.125

	SC_12_AA	African American	24	IG		0.583	0.417			0.371	0.792	0.208

	SC_12_C	European	12	IG		0.167	0.667		0.167	0.439	0.500	0.500

	SC_95_C	European	86	IG		0.209	0.674		0.116	0.020	0.547	0.453

	HapMap-CEU	European	118	IG		0.441	0.508		0.051	0.251	0.695	0.305

	HapMap-HCB	Asian	90	IG		0.956	0.044			1.000	0.978	0.022

	HapMap-JPT	Asian	90	IG		0.822	0.178			0.527	0.911	0.089

	HapMap-YRI	Sub-Saharan African	120	IG		0.367	0.517		0.117	0.439	0.625	0.375

	CHMJ	Asian	74	IG	0.959			0.041			0.959	0.041

ss24596928	AFD_EUR_PANEL	European	46	IG		0.348	0.609		0.043	0.150	0.652	0.348

	AFD_AFR_PANEL	African American	44	IG		0.545	0.455			0.200	0.773	0.227

	AFD_CHN_PANEL	Asian	48	IG		0.917	0.083			1.000	0.958	0.042

ss44042833	AoD_African_American		90	AF							0.640	0.360

	AoD_Caucasian		92	AF							0.730	0.270

	AoD_Chinese		90	AF							0.940	0.060

	AoD_Japanese		90	AF							0.950	0.050

ss66286489	HapMap-CEU	European	118	GF		0.424	0.508		0.068		0.678	0.322

	HapMap-HCB	Asian	90	GF		0.956	0.044				0.978	0.022

	HapMap-JPT	Asian	90	GF		0.822	0.178				0.911	0.089

	HapMap-YRI	Sub-Saharan African	120	GF		0.367	0.517		0.117		0.625	0.375

ss69193632	HapMap-CEU	European	120	GF		0.433	0.500		0.067		0.683	0.317

	HapMap-HCB	Asian	90	GF		0.956	0.044				0.978	0.022

	HapMap-JPT	Asian	90	GF		0.822	0.178				0.911	0.089

	HapMap-YRI	Sub-Saharan African	120	GF		0.367	0.517		0.117		0.625	0.375

ss75947635	ICMHP		8	IG		0.500	0.500				0.750	0.250

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss1315276	1280	642	493	111
ss24596928	71
ss66286489	262	148	94	20
ss69193632	263
ss75947635	6	3	3
ss96540036	1

RefSNP Genotype Summary	Total Individual	G	G/G	G/T	T	T/T
rs887241	1333		654	502		112

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
150	ss1315276	G/T	TSC-CSHL	SC_95_C	CEPH1334.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
150	ss1315276	G/G	CSHL-HAPMAP	HapMap-CEU	NA10846	CEPH1334.01	r27_ch17_CEU_affymetrix:genomewidesnp_6.0	844699
150	ss66286489	G/G	CSHL-HAPMAP	HapMap-CEU	NA10846	CEPH1334.01	chr17-HapMap-CEU
150	ss69193632	C/C	CSHL-HAPMAP	HapMap-CEU	NA10846	CEPH1334.01	chr17-HapMap-CEU
161	ss1315276	G/T	TSC-CSHL	SC_95_C	CEPH1340.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
161	ss1315276	G/G	CSHL-HAPMAP	HapMap-CEU	NA07029	CEPH1340.01	r27_ch17_CEU_affymetrix:genomewidesnp_6.0	844699
161	ss66286489	G/G	CSHL-HAPMAP	HapMap-CEU	NA07029	CEPH1340.01	chr17-HapMap-CEU
161	ss69193632	C/C	CSHL-HAPMAP	HapMap-CEU	NA07029	CEPH1340.01	chr17-HapMap-CEU
225	ss1315276	G/T	TSC-CSHL	SC_95_C	CEPH1346.11		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
225	ss1315276	G/G	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch17_CEU_affymetrix:genomewidesnp_6.0	844699
225	ss66286489	G/G	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	chr17-HapMap-CEU
225	ss69193632	C/C	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	chr17-HapMap-CEU
229	ss1315276	G/T	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
229	ss1315276	T/T	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844699
229	ss1315276	G/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r27_ch17_CEU_affymetrix:genomewidesnp_6.0	844699
229	ss66286489	G/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr17-HapMap-CEU
229	ss69193632	A/C	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr17-HapMap-CEU
230	ss1315276	G/T	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844699
230	ss1315276	T/T	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
231	ss1315276	G/G	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844699
231	ss1315276	T/T	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
360	ss1315276	G/T	TSC-CSHL	SC_95_C	CEPH1362.13		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
360	ss1315276	G/G	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	r27_ch17_CEU_affymetrix:genomewidesnp_6.0	844699
360	ss66286489	G/G	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	chr17-HapMap-CEU
360	ss69193632	C/C	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	chr17-HapMap-CEU
429	ss1315276	G/T	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	844699
429	ss1315276	N/N	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
429	ss1315276	T/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r27_ch17_CEU_affymetrix:genomewidesnp_6.0	844699
429	ss66286489	T/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr17-HapMap-CEU
429	ss69193632	A/A	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr17-HapMap-CEU
464	ss1315276	G/T	TSC-CSHL	SC_95_C	CEPH1420.09		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	844699
464	ss1315276	G/G	CSHL-HAPMAP	HapMap-CEU	NA12003	CEPH1420.09	r27_ch17_CEU_affymetrix:genomewidesnp_6.0	844699
464	ss66286489	G/G	CSHL-HAPMAP	HapMap-CEU	NA12003	CEPH1420.09	chr17-HapMap-CEU
464	ss69193632	C/C	CSHL-HAPMAP	HapMap-CEU	NA12003	CEPH1420.09	chr17-HapMap-CEU

Genotype data submitted for	1415	samples from	1333	individuals	Individual with multiple genotypes submission:	294

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .