Reference SNP(refSNP) Cluster Report: rs937838

Reference SNP(refSNP) Cluster Report: rs937838

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

HGVS Names
NM_003241.3:c.746G>C
NP_003232.2:p.Ser249Thr
NT_022517.17:g.44883108G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48406449 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs937838 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
ss1377860	TSC-CSHL\|TSC0356651	fwd/T	C/G	gtggcacagccccatacaagtggacaggca	tgccccgatcctgcagcagtactacaacac	09/06/00	04/07/04	86	Genomic	95 %
ss3234747	YUSUKE\|IMS-JST044832	fwd/T	C/G	gtggcacagccccatacaagtggacaggca	tgccccgatcctgcagcagtactacaacac	09/05/01	10/10/03	100	Genomic	unknown
ss48406449	APPLERA_GI\|hCV9489643	fwd/	C/G	gtggcacagccccatacaagtggacaggca	tgccccgatcctgcagcagtactacaacac	09/28/05	11/03/06	126	Genomic	unknown
ss68860336	PERLEGEN\|PGP04609730	fwd/	C/G	gtggcacagccccatacaagtggacaggca	tgccccgatcctgcagcagtactacaacac	01/30/07	08/14/07	127	Genomic	unknown
ss74807505	AFFY\|SNP_M-178787	fwd/T	C/G	gtggcacagccccatacaagtggacaggca	tgccccgatcctgcagcagtactacaacac	08/09/07	08/09/07	128	Genomic	unknown

Fasta sequence (Legend)

 ATACAGCAGT GAGCATCCTC CCCGGTCACT CAAACAGCTG GCATGCTCCT TGGCCCTTCT
 GGGCACCCCA CCTGTTCTGG AAAGCCCACG TCCTCCAAGT ACTCTGAGAC ATTATGAGGT
 GTCCACTTTG GGGGCTGGGT GGCCAAGCTG GGCTGGCAGC ACCTTGTTCT TCTGAGGGGC
 GGACACTGAC CCCACCCCTA CGTGTGTGGC AGATGAGCTT TGAGAAAGGC CAGGGCGTGC
 TCATTGGGAA TTGGACTGGG GACTACGAAG GTGGCACAGC CCCATACAAG TGGACAGGCA
 S
 TGCCCCGATC CTGCAGCAGT ACTACAACAC GAAGCAGGCT GTGTGCTTTG GCCAGTGCTG
 GGTGTTTGCT GGGATCCTGA CTACAGGTAA GTGGCAGATC CAGGGGCTGA GGGGAGAGGT
 CCCAAGGGAG GGACTCCCAG CCCCCACAGT TGCCAACCAC CCCACCCTGG ATCATTTCAG
 TGCTGAGAGC GTTGGGCATC CCAGCACGCA GTGTGACAGG CTTCGATTCA GCTCACGACA
 CAGAAAGGAA CCTCACGGTG GACACCTATG TGAATGAGAA TGGCGAGAAA ATCACCAGTA

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
NC_000003.9

dbSNP Blast Analysis

UniGene Cluster ID
438265

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss1377860	SC_12_A	Asian	20	IG			1.000			1.000

	SC_12_AA	African American	22	IG		0.091	0.909	1.000	0.045	0.955

	SC_12_C	European	14	IG		0.429	0.571	0.479	0.214	0.786

	SC_95_C	European	92	IG	0.022	0.304	0.674	0.752	0.174	0.826

	CEPH		184	AF					0.230	0.770

ss3234747	JBIC-allele		1504	AF					0.037	0.963

ss48406449	HapMap-CEU	European	120	IG		0.250	0.750	0.273	0.125	0.875

	HapMap-HCB	Asian	90	IG		0.044	0.956	1.000	0.022	0.978

	HapMap-JPT	Asian	88	IG		0.091	0.909	0.752	0.045	0.955

	HapMap-YRI	Sub-Saharan African	120	IG		0.100	0.900	0.752	0.050	0.950

	AGI_ASP population	multiple	66	IG		0.061	0.939	1.000	0.030	0.970

ss68860336	HapMap-CEU	European	120	GF		0.250	0.750		0.125	0.875

	HapMap-HCB	Asian	90	GF		0.044	0.956		0.022	0.978

	HapMap-JPT	Asian	90	GF		0.089	0.911		0.044	0.956

	HapMap-YRI	Sub-Saharan African	120	GF		0.100	0.900		0.050	0.950

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss1377860	121	3	27	87
ss48406449	557		39	262
ss68860336	269		37	231

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs937838	631	3	50	323

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
230	ss1377860	C/G	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
230	ss1377860	G/G	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
231	ss1377860	C/G	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
231	ss1377860	G/G	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429	ss1377860	C/C	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429	ss1377860	C/G	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
429	ss48406449	C/C	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r27_ch3_CEU_bcm:genotype_0002
429	ss68860336	C/C	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr3-HapMap-CEU
430	ss1377860	C/G	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
430	ss1377860	G/G	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE

Genotype data submitted for	689	samples from	631	individuals	Individual with multiple genotypes submission:	281

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 .