Reference SNP(refSNP) Cluster Report: rs3733182

Reference SNP(refSNP) Cluster Report: rs3733182

refSNP ID: rs3733182
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
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_018401.1:c.592A>G
NP_060871.1:p.R198G
NT_006051.17:g.1535873A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44558182 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3733182 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
ss4919177	YUSUKE\|IMS-JST086813	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	07/24/02	10/10/03	107	Genomic	unknown
ss24163530	PERLEGEN\|afd0635075	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	08/10/04	09/13/04	123	Genomic	unknown
ss28498608	MGC_GENOME_DIFF\|37540616-A1535874G	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	08/20/04	08/20/04	126	cDNA	unknown
ss28513542	MGC_GENOME_DIFF\|BC038238x37540616-A1535874G	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	08/25/04	08/25/04	126	cDNA	unknown
ss44558182	ABI\|hCV2971952	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	07/19/05	11/03/06	126	Genomic	unknown
ss48534042	CANCER-GENOME\|NC_000004.9_5566501	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	10/20/05	11/29/05	126	Genomic	unknown
ss65727512	ILLUMINA\|Human1-rs3733182	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	10/10/06	10/10/06	127	Genomic	unknown
ss66616394	ILLUMINA\|HumanHap300v1.1_rs3733182	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	11/09/06	11/09/06	127	Genomic	unknown
ss67297587	ILLUMINA\|HumanHap550v1.1_rs3733182	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	11/14/06	11/14/06	127	Genomic	unknown
ss67702117	ILLUMINA\|HumanHap650Yv1.0_rs3733182	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	11/14/06	11/14/06	127	Genomic	unknown
ss68888999	PERLEGEN\|PGP00635075	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	01/30/07	03/31/08	127	Genomic	unknown
ss70776215	ILLUMINA\|HumanHap550v3.0__rs3733182	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	04/20/07	03/30/08	130	Genomic	unknown
ss71352284	ILLUMINA\|HumanHap650Yv3.0_rs3733182	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	04/23/07	04/23/07	127	Genomic	unknown
ss74813016	AFFY\|SNP_M-288887	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	08/09/07	08/09/07	128	Genomic	unknown
ss75431620	ILLUMINA\|ILMN_Human_1M_rs3733182	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	08/28/07	08/29/07	129	Genomic	unknown
ss79163264	ILLUMINA\|HumanHap300v2.0_rs3733182	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	04/18/07	11/18/07	130	Genomic	unknown
ss84158854	KRIBB_YJKIM\|KHS647528	fwd/B	C/T	agtcgacagggtacgagtatccggggcctc	gtccatgtacacctggaatacttctggagc	12/04/07	12/06/07	130	Genomic	unknown
ss86270267	CORNELL\|hCV2971952	rev/T	A/G	gctccagaagtattccaggtgtacatggac	gaggccccggatactcgtaccctgtcgact	01/21/08	01/21/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCTCCCCCAC TGAATGCCTC TTTCCCATCT GTACAATGAG TGGGTTGGAC CAGAAGTTCA
 GGGCGTTCAT AGGCGGCACA CAGGCATCAG GACTGAAACC TGGGGGGCAG TGACTCCCCC
 AGTGCTCCTT CCTGCACCGC GGGCCCTGCC GACTCTGCCC GTCCAGGTAC AACGTGAGCC
 CCCACTGCAC AGCCCCTCGT GTGTACCGCA CAGGTGCCTG TCTTACCCAG CCCCGCAGCA
 GCTCATAGGC TGTGATGCCC AGGGACCACC AGTCGACAGG GTACGAGTAT CCGGGGCCTC
 Y
 GTCCATGTAC ACCTGGAATA CTTCTGGAGC TGCCAACGAG AGGACAAGGA GAACATCATT
 GTGTATCCCA GTTTATGGCC ACCACCCCTT AGAGAGGGGA CAAGGAGAGA AATTGAGCTT
 GTTTTTTTTT TTTTTGTTTT TTTTTGAGAT AGAGTTTTGC TCTGCTGCCC AGGCTGGCAC
 ATAATGGCGC AATGTCGGCT CCTCTGTGCC TTAGTTCAAG CGATTCTCCT TCCTCAGCCT
 GCCGAGCAGC TGAGATTACA GGCACCTGCC ACCATGCCTG GCTAATTGTG ATATTTTTAG

GeneView

GeneView via analysis of contig annotation: STK32B serine/threonine kinase 32B

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_006051->NM_018401

function

HuRef

NW_001838897->NM_018401

function

Celera

NW_921918->NM_018401

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_006051->NM_018401->NP_060871	1535874	forward	656	missense	G	Gly [G]	1	198
					contig reference	A	Arg [R]	1	198

HuRef	NW_001838897->NM_018401->NP_060871	1630016	forward	656	missense	G	Gly [G]	1	198
					contig reference	A	Arg [R]	1	198

Celera	NW_921918->NM_018401->NP_060871	5346086	forward	656	missense	G	Gly [G]	1	198
					contig reference	A	Arg [R]	1	198

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3733182 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_921918.1	5346086	5346086	minus	A	alt_assembly_1	Celera	Celera	view	300
4	NW_001838897.1	1630016	5384249	minus	A	alt_assembly_8	HuRef	HuRef	view	300
4	NT_006051.17	1535874	5499330	minus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006051.1 BC038238

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC004664.1 NC_000004.10	AC004661.2

UniGene Cluster ID
133062

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24163530	AFD_EUR_PANEL	European	42	IG		0.095	0.905	1.000	0.048	0.952

	AFD_AFR_PANEL	African American	38	IG	0.053	0.474	0.474	0.527	0.289	0.711

	AFD_CHN_PANEL	Asian	34	IG	0.059	0.706	0.235	0.100	0.412	0.588

ss44558182	HapMap-CEU	European	120	IG		0.167	0.833	0.527	0.083	0.917

	HapMap-HCB	Asian	90	IG	0.222	0.400	0.378	0.251	0.422	0.578

	HapMap-JPT	Asian	88	IG	0.205	0.591	0.205	0.251	0.500	0.500

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.233	0.750	1.000	0.133	0.867

	AoD_African_American		90	AF					0.210	0.790

	AoD_Caucasian		92	AF					0.120	0.880

ss4919177	JBIC-allele		1480	AF					0.471	0.529

ss68888999	HapMap-CEU	European	120	GF		0.150	0.850		0.075	0.925

	HapMap-HCB	Asian	90	GF	0.222	0.400	0.378		0.422	0.578

	HapMap-JPT	Asian	90	GF	0.200	0.600	0.200		0.500	0.500

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.217	0.767		0.125	0.875

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24163530	71
ss44558182	268
ss68888999	268

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs3733182	332

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
226	ss44558182	A/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r23_ch4_CEU_illumina:golden_gate_1.0.0	460911
226	ss68888999	A/A	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	chr4-HapMap-CEU
5276	ss44558182	A/G	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	r23_ch4_YRI_illumina:golden_gate_1.0.0	460911
5276	ss68888999	A/A	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	chr4-HapMap-YRI

Genotype data submitted for	341	samples from	332	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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .