Reference SNP(refSNP) Cluster Report: rs743686

Reference SNP(refSNP) Cluster Report: rs743686

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

HGVS Names
NM_002280.4:c.106T>C
NP_002271.3:p.Ser36Pro
NT_010755.15:g.3361540A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss92903 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs743686 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
ss92903	TSC-CSHL\|TSC0116960	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	09/06/00	04/07/04	86	Genomic	95 %
ss10849141	BCM_SSAHASNP\|chr17.NT_010755.13_3359966	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	06/30/03	10/10/03	116	Genomic	unknown
ss14282370	BCM_SSAHASNP\|chr17.NT_010755.14_3359742	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	11/05/03	11/22/03	119	Genomic	unknown
ss16748625	CSHL-HAPMAP\|CSHL-HuAA-200402.chr17.NT_010755.14_3359742	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	02/17/04	03/04/04	120	Genomic	unknown
ss20039161	CSHL-HAPMAP\|CSHL-HuFF-200402.chr17.NT_010755.14_3359742	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	02/21/04	03/04/04	120	Genomic	unknown
ss21395386	SSAHASNP\|WGSA-200403-chr17.chr17.NT_010755.14_3359742	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	03/19/04	03/20/04	121	Genomic	unknown
ss24562380	PERLEGEN\|afd2543763	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	08/10/04	09/13/04	123	Genomic	unknown
ss44014856	ABI\|hCV11939309	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	07/18/05	07/18/05	126	Genomic	unknown
ss65729394	ILLUMINA\|Human1-rs743686	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	10/10/06	10/10/06	127	Genomic	unknown
ss66594380	ILLUMINA\|HumanHap300v1.1_rs743686	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	11/09/06	11/09/06	127	Genomic	unknown
ss67578736	ILLUMINA\|HumanHap550v1.1_rs743686	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	11/14/06	11/14/06	127	Genomic	unknown
ss67960416	ILLUMINA\|HumanHap650Yv1.0_rs743686	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	11/14/06	11/15/06	127	Genomic	unknown
ss69196317	PERLEGEN\|PGP02543763	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	01/30/07	08/14/07	127	Genomic	unknown
ss70927948	ILLUMINA\|HumanHap550v3.0__rs743686	rev/B	C/T	actcgtgtgtccgcaatgtactccagcagc	cttgcaagcttccaagtctctcccctgtgg	04/20/07	03/31/08	130	Genomic	unknown
ss71529103	ILLUMINA\|HumanHap650Yv3.0_rs743686	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	04/23/07	04/23/07	127	Genomic	unknown
ss74807271	AFFY\|SNP_M-177979	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	08/09/07	08/09/07	128	Genomic	unknown
ss74944073	ILLUMINA\|ILMN_Human_1M_rs743686	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	08/28/07	08/29/07	129	Genomic	unknown
ss77773641	HGSV\|Cor12156_SNV_20070510.chr17_36890770	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	10/09/07	10/14/07	129	Genomic	unknown
ss78727336	HGSV\|Cor12878_SNV_20070510.chr17_36890770	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	10/17/07	10/20/07	129	Genomic	unknown
ss79257108	ILLUMINA\|HumanHap300v2.0_rs743686	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	04/18/07	11/18/07	130	Genomic	unknown
ss83545444	KRIBB_YJKIM\|KHS486561	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	12/04/07	12/05/07	130	Genomic	unknown
ss84205551	HGSV\|Cor18555_SNV_20070510.chr17_36890770	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	11/27/07	12/06/07	130	Genomic	unknown
ss96545776	HUMANGENOME_JCVI\|1103645324516	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	03/26/08	03/26/08	130	Genomic	unknown
ss109763460	1000GENOMES\|CEU.trio.12.15.2008_3398612_chr17_36890770	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	12/15/08	12/16/08	130	Genomic	unknown
ss113531504	1000GENOMES\|NA19240_2008_12_16_3057703_chr17_36890770	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	12/18/08	12/18/08	130	Genomic	unknown
ss118054131	ILLUMINA-UK\|NA18507_000043134_NCBI36.1_chr17_36890770	fwd/T	A/G	ccacaggggagagacttggaagcttgcaag	gctgctggagtacattgcggacacacgagt	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 GTGGCCCTGT AGCTGCTTCT GCCCAGACCC ACTGAGCAGG CAGAGAAACT TCTGGCCACA
 GGGGAGAGAC TTGGAAGCTT GCAAG
 R
 GCTGCTGGAG TACATTGCGG ACACACGAGT GGAGCCCCCA CTGGCCCCTC CTGGGCTCTT
 GAGAGACCCA GAAGAGAAGC CGGCCTTGAG GCATTTGGAA GCCATGGCCC CTGCAACTCA
 GATGCAATTG ATAGGTCTCT GAGGCCAGAC ACCCCAAAGC AGAGAAGCAG CTCCTTACCC
 CAGATTTATA TCTCTGCCCC AGTGGGCATT GGTTGGCCTT TACAAAGTGT TTTCTCCTCA
 TTAAAGTTAA CACCACTTTC TATTAAAACC CCTCATTAAC CTGTTATTTA GTTTCCTGTG
 AAAATTTACC AGTCTCATAA AATAGGAGCC CCATTACTAT GTCAAGACTC ATCTCCACCA
 CCCCACATCA CTGGGAAGAC CAAGTCCCTG TCAGTTCTTC AAAGGGACCT GTCATTTGAG
 CCCAGACCTC AGCCTCCGCA TTAAGCAAGC ATGGGAGTTC AGCCACTGTC TTGACTTTCT
 CCAACTTTGA CTTCTTTTAT TGGCCTGAGG GAGTAGAGGA GGTCTCTGGG GTGCTCCCAG
 AAGATGGAGG GTAAACTTGG TTGGTGCAGG AAGGCAGGGG TCTTGCGGCC AGGGAGACAC
 AGAAGGCTCT TGAATTGGCC CAGAAAAATG GCTAAGTGAC CAATTTTTTT GGTTTCCCAA
 GGATTTTCTG GCTTTAGTTC CCAAAGTTCC ATATGCCAGG GAAACCTTAG TCCTGGTAAA
 ATGGGGCAGC TTATTACCCT AATACT

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_010755 ABBA01031810

dbSNP Blast Analysis

UniGene Cluster ID
73082

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A	A/A	A/G	G	G/G	N	HWP	A	G	N
ss24562380	AFD_EUR_PANEL	European	48	IG		0.292	0.583		0.125		0.343	0.583	0.417

	AFD_AFR_PANEL	African American	46	IG		0.087	0.348		0.565		0.655	0.261	0.739

	AFD_CHN_PANEL	Asian	48	IG		0.458	0.500		0.042		0.317	0.708	0.292

ss69196317	HapMap-CEU	European	120	GF		0.317	0.467		0.217			0.550	0.450

	HapMap-HCB	Asian	90	GF		0.422	0.489		0.089			0.667	0.333

	HapMap-JPT	Asian	90	GF		0.444	0.444		0.111			0.667	0.333

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

ss92903	SC_12_A	Asian	24	IG		0.583	0.250		0.167		0.200	0.708	0.292

	SC_12_AA	African American	18	IG			0.556		0.444		0.251	0.278	0.722

	SC_12_C	European	14	IG		0.286	0.571		0.143		0.752	0.571	0.429

	SC_95_C	European	90	IG		0.422	0.422		0.156		0.584	0.633	0.367

	CEPH		184	AF								0.470	0.530

	HapMap-CEU	European	120	IG		0.317	0.467		0.217		0.752	0.550	0.450

	HapMap-HCB	Asian	90	IG		0.422	0.467		0.111		1.000	0.656	0.344

	HapMap-JPT	Asian	88	IG		0.477	0.409		0.114		0.752	0.682	0.318

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

	CHMJ	Asian	74	IG	0.743			0.243		0.014		0.743	0.243	0.014

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24562380	71	20	34	17
ss69196317	266	72	113	81
ss92903	1282	241	530	484
ss96545776	1			1

RefSNP Genotype Summary	Total Individual	A	A/A	A/G	G	G/G	N
rs743686	1328		261	553		506

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
229	ss92903	A/A	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss92903	A/G	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229	ss92903	A/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r27_ch17_CEU_illumina:human_1m_beadchip
229	ss69196317	A/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr17-HapMap-CEU
231	ss92903	A/A	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
231	ss92903	A/G	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
430	ss92903	A/G	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
430	ss92903	G/G	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
5157	ss92903	N/N	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	r27_ch17_CHB_illumina:human_1m_beadchip
5157	ss69196317	A/G	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	chr17-HapMap-HCB
5205	ss92903	A/A	CSHL-HAPMAP	HapMap-JPT	NA18953	JA18953	r27_ch17_JPT_illumina:human_1m_beadchip
5205	ss69196317	A/G	CSHL-HAPMAP	HapMap-JPT	NA18953	JA18953	chr17-HapMap-JPT
5223	ss92903	A/A	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	r27_ch17_JPT_illumina:human_1m_beadchip
5223	ss69196317	A/G	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	chr17-HapMap-JPT

Genotype data submitted for	1410	samples from	1328	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 .