Reference SNP(refSNP) Cluster Report: rs1937839

Reference SNP(refSNP) Cluster Report: rs1937839

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	92/130
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_003739.4:c.459G>A
NT_077567.3:g.5081530G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss105434909 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1937839 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	Ancestral Allele	Success Rate
ss2827704	TSC-CSHL\|TSC1005562	fwd/B	C/T	aatggacttggccaatcctgcatccttaca	ttctccatggcctgtggagaaaggggttgt	01/03/01	10/10/03	92	Genomic		unknown
ss23561190	PERLEGEN\|afd2201832	rev/T	A/G	acaacccctttctccacaggccatggagaa	tgtaaggatgcaggattggccaagtccatt	08/10/04	09/13/04	123	Genomic		unknown
ss38343032	CEPH\|G9-SN-E5S4	rev/T	A/G	acaacccctttctccacaggccatggagaa	tgtaaggatgcaggattggccaagtccatt	05/19/05	05/19/05	125	Genomic	G	100 %
ss39783349	ABI\|hCV11376576	rev/T	A/G	acaacccctttctccacaggccatggagaa	tgtaaggatgcaggattggccaagtccatt	07/16/05	11/02/06	126	Genomic		unknown
ss86237234	CORNELL\|hCV11376576	rev/T	A/G	acaacccctttctccacaggccatggagaa	tgtaaggatgcaggattggccaagtccatt	01/21/08	01/21/08	129	Genomic		unknown
ss105434909	SNP500CANCER\|AKR1C3-18	rev/T	A/G	acaacccctttctccacaggccatggagaa	tgtaaggatgcaggattggccaagtccatt	09/05/08	09/05/08	130	Genomic		unknown

Fasta sequence (Legend)

 TTTTTCCCTA ATACTTTTCC AAGCAGGGTA CAAACAAGAA ATCTTCACGC CTTTCTTGAC
 AGAAGCTTTG CTCTCTAGAT AATCTTCTAC TTYACAAAGA TAACTGGGAC AAAACAAACA
 GATATTTGGC AATAGGACAG GAAGAGGGGG CATGAAGAAC CGAAAGGAGA GAAGGCCAAG
 GGAGCTCACC TGGTTGCAGA CAGGCTTGTA CTTRAGTCCT GRCTTGTTGA GGATSATCTC
 CAGCTGCCTG CRGTTGAAGT TTGAYACCCC AATGGACTTG GCCAATCCTG CATCCTTACA
 Y
 TTCTCCATGG CCTGTGGAGA AAGGGGTTGT GAGGAATTAT TTGTGCAGTT GGCTGCAAAT
 CACRGTAAAT GCAAGACAGA ACTGTGAGAR CAACAACTTT CAAAGTATGA CAATGNAAAA
 TAGCTAGCAG TGATTGTCAA AAAAAGAAAA ATTCAAACAG CAAATAGGGG AAGAAGATAG
 AGGCAGCAAG AGTAAGAATT TCTATCTCTT CCTTAGGAAA CTGSATAGAT TAATGCAYAA
 GYAAGGAAAG AGATTCCTGT CCTCCTTGMC CCCAAGTCTT GTGCCCCACT CTCTAAACAT
 T

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_000010.5

dbSNP Blast Analysis

UniGene Cluster ID
78183

3D structure mapping
NP_003730

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss105434909	P1		200	GF	0.980	0.020			0.990	0.010

	CAUC1		58	GF	1.000				1.000

	AFR1		48	GF	0.917	0.083			0.958	0.042

	HISP1		46	GF	1.000				1.000

	PAC1		48	GF	1.000				1.000

	P3		514	GF	0.949	0.047	0.004		0.973	0.027

	CAUC3		130	GF	1.000				1.000

	AFR3		138	GF	0.812	0.174	0.014		0.899	0.101

	HISP3		96	GF	1.000				1.000

	PAC3		150	GF	1.000				1.000

ss23561190	AFD_EUR_PANEL	European	48	IG	1.000				1.000

	AFD_AFR_PANEL	African American	46	IG	0.826	0.174		0.655	0.913	0.087

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

ss2827704	C		84	AF					1.000

	B		84	AF					1.000

	A		84	AF					1.000

	CEPH-TRIOS		606	AF					1.000

ss39783349	HapMap-CEU	European	120	IG	1.000				1.000

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.850	0.150		0.584	0.925	0.075

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.044+/-0.142	581	459	15	0

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 .