Reference SNP(refSNP) Cluster Report: rs315914

Reference SNP(refSNP) Cluster Report: rs315914

refSNP ID: rs315914
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44662246 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs315914 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
ss404877	KWOK\|OVLP-000621-256453	rev/B	C/T	actcccatggggtaaggaagaccgcagcat	caagtcggcagtgctgttgtcctgaactgg	06/30/00	10/10/03	79	Genomic	99 %
ss567672	SC_JCM\|AC025775.3_63505	rev/B	C/T	actcccatggggtaaggaagaccgcagcat	caagtcggcagtgctgttgtcctgaactgg	07/12/00	10/10/03	80	Genomic	unknown
ss971476	KWOK\|OVLP-000804-520834	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	09/01/00	10/10/03	86	Genomic	99 %
ss1361290	TSC-CSHL\|TSC0239314	rev/B	C/T	actcccatggggtaaggaagaccgcagcat	caagtcggcagtgctgttgtcctgaactgg	09/06/00	10/10/03	86	Genomic	95 %
ss1616474	KWOK\|OVLP-000925-511973	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	10/04/00	10/25/06	87	Genomic	99 %
ss5966573	SC_JCM\|NT_023089.10_260252	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	01/10/03	10/10/03	111	Genomic	unknown
ss22280258	SSAHASNP\|WGSA-200403-chr5.chr5.NT_023089.13_2400826	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	03/21/04	03/21/04	121	Genomic	unknown
ss44662246	ABI\|hCV1002059	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	07/19/05	11/03/06	126	Genomic	unknown
ss66259407	AFFY\|SNP_A-4289422	fwd/T	A/G	cagcactgccgacttg	atgctgcggtcttcct	10/27/06	08/14/07	127	Genomic	unknown
ss66543944	ILLUMINA\|HumanHap300v1.1_rs315914	fwd/B	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	11/09/06	11/09/06	127	Genomic	unknown
ss67292074	ILLUMINA\|HumanHap550v1.1_rs315914	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	11/14/06	11/14/06	127	Genomic	unknown
ss67695771	ILLUMINA\|HumanHap650Yv1.0_rs315914	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	11/14/06	11/14/06	127	Genomic	unknown
ss68924282	PERLEGEN\|PGP02591398	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	01/30/07	08/14/07	127	Genomic	unknown
ss70770667	ILLUMINA\|HumanHap550v3.0__rs315914	rev/B	C/T	actcccatggggtaaggaagaccgcagcat	caagtcggcagtgctgttgtcctgaactgg	04/20/07	03/30/08	130	Genomic	unknown
ss71345907	ILLUMINA\|HumanHap650Yv3.0_rs315914	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	04/23/07	04/23/07	127	Genomic	unknown
ss75074312	ILLUMINA\|ILMN_Human_1M_rs315914	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	08/28/07	08/29/07	129	Genomic	unknown
ss76404611	AFFY\|AFFY_6_1M_SNP_A-4289422	fwd/T	A/G	cagcactgccgacttg	atgctgcggtcttcct	08/28/07	08/30/07	129	Genomic	unknown
ss79159538	ILLUMINA\|HumanHap300v2.0_rs315914	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	04/18/07	11/18/07	130	Genomic	unknown
ss83424188	KRIBB_YJKIM\|KHS458342	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	12/04/07	12/05/07	130	Genomic	unknown
ss92963264	BCMHGSC_JDW\|JWB-1923914	fwd/T	A/G	ccagttcaggacaacagcactgccgacttg	atgctgcggtcttccttaccccatgggagt	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 GTCCAGAGCC CCCTTTCGAG AAGTTCCAAG TTCTGTCTCC TGGGCTGCAG TGACCAGAGG
 GTCGTTTCCC ATCTGACTCT ATGCACTGGG CTCAAGAGGG TACCAGGGGT GGAAGCCTGC
 CAGGGTACAT CTATGTGATG GGGGCTGGAC AGCCAGTTCA GTATTTTAGG GAGCTTGAAA
 GAAAGCCGTT ACATACACAA CGCATTAAGG GGTGCTGGCA CAACCTACTC CTAAGCCAAC
 TGAAATATAG CCGCCTTATC TTCCTACAGA CCAGTTCAGG ACAACAGCAC TGCCGACTTG
 R
 ATGCTGCGGT CTTCCTTACC CCATGGGAGT ATGGGGACAC ATGAGGTTTT GAAGCCTGGG
 TTCTGGGCAC AAGAGCTAAA CAGGCTTGAT GGTATGGCAT TTTGGGAGCT GAGGTGCAGG
 GCTAAGGAAA GGCTAGGCCT GTGATGCTGG GGCCTGGAGG TGGGGTGGGT CCCTCCTGCA
 GCAGAGACCT GCCAGTCAGT CCCAACAGCC CCCCAAGGAA CCAGGGCTCC AGAATCGCTG
 GTGCATGCAT GGGACAGAGC AAAATGCTAA GTGTCACTGC TTTGGGCTTG CCAGTGGCAC

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs315914 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838924.2	902267	2395564	minus	C	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922518.1	1552676	2450244	plus	A	alt_assembly_1	Celera	Celera	view	300
5	NT_006576.15	2408088	2471088	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023089.10 AC025228 AC025775.3 AC026709.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC025775.6 AC026709.7 NC_000005.8	AC025228.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss44662246	HapMap-CEU	European	118	IG	0.339	0.424	0.237	0.251	0.551	0.449

	HapMap-HCB	Asian	90	IG	0.022	0.467	0.511	0.150	0.256	0.744

	HapMap-JPT	Asian	88	IG	0.091	0.386	0.523	0.584	0.284	0.716

	HapMap-YRI	Sub-Saharan African	120	IG	0.100	0.300	0.600	0.150	0.250	0.750

ss66259407	HapMap-CEU	European	118	GF	0.339	0.424	0.237		0.551	0.449

	HapMap-HCB	Asian	90	GF	0.044	0.444	0.511		0.267	0.733

	HapMap-JPT	Asian	90	GF	0.200	0.289	0.511		0.344	0.656

	HapMap-YRI	Sub-Saharan African	120	GF	0.100	0.300	0.600		0.250	0.750

ss68924282	HapMap-CEU	European	120	GF	0.350	0.417	0.233		0.558	0.442

	HapMap-HCB	Asian	90	GF	0.022	0.467	0.511		0.256	0.744

	HapMap-JPT	Asian	90	GF	0.111	0.378	0.511		0.300	0.700

	HapMap-YRI	Sub-Saharan African	120	GF	0.100	0.300	0.600		0.250	0.750

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss44662246	263	44	100	117
ss66259407	262	45	100	117
ss68924282	263	46	100	117

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs315914	270	46	100	117

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
611	ss44662246	A/G	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	r23_ch5_CEU_affymetrix:genotype_protocol_1
611	ss66259407	A/G	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	chr5-HapMap-CEU
611	ss68924282	G/G	CSHL-HAPMAP	HapMap-CEU	NA12865	CEPH1459.02	chr5-HapMap-CEU
5169	ss44662246	A/G	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	r23_ch5_HCB_affymetrix:genotype_protocol_1
5169	ss66259407	A/A	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	chr5-HapMap-HCB
5169	ss68924282	A/G	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	chr5-HapMap-HCB
5210	ss44662246	A/G	CSHL-HAPMAP	HapMap-JPT	NA18961	JA18961	r23_ch5_JPT_affymetrix:genotype_protocol_1
5210	ss66259407	A/A	CSHL-HAPMAP	HapMap-JPT	NA18961	JA18961	chr5-HapMap-JPT
5210	ss68924282	A/G	CSHL-HAPMAP	HapMap-JPT	NA18961	JA18961	chr5-HapMap-JPT
5211	ss44662246	A/G	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	r23_ch5_JPT_affymetrix:genotype_protocol_1
5211	ss66259407	A/A	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	chr5-HapMap-JPT
5211	ss68924282	A/G	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	chr5-HapMap-JPT
5212	ss44662246	A/G	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	r23_ch5_JPT_affymetrix:genotype_protocol_1
5212	ss66259407	A/A	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	chr5-HapMap-JPT
5212	ss68924282	A/G	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	chr5-HapMap-JPT
5222	ss44662246	A/G	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r23_ch5_JPT_affymetrix:genotype_protocol_1
5222	ss66259407	A/A	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	chr5-HapMap-JPT
5222	ss68924282	A/G	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	chr5-HapMap-JPT
5244	ss44662246	A/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	r23_ch5_YRI_affymetrix:genotype_protocol_1
5244	ss66259407	A/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	chr5-HapMap-YRI
5244	ss68924282	A/A	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	chr5-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	270

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .