Reference SNP(refSNP) Cluster Report: rs3748140

Reference SNP(refSNP) Cluster Report: rs3748140

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/130
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_024607.2:c.143G>A
NP_078883.2:p.Gly48Glu

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76889558 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3748140 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
ss4934163	YUSUKE\|IMS-JST099863	fwd/T	A/G	ttcagctgagcagcaagaatgaagccagtg	aatggtggccccggctgtccaggagaagaa	08/01/02	10/10/03	107	Genomic	unknown
ss23953336	PERLEGEN\|afd1861296	rev/B	C/T	ttcttctcctggacagccggggccaccatt	cactggcttcattcttgctgctcagctgaa	08/10/04	09/13/04	123	Genomic	unknown
ss69038880	PERLEGEN\|PGP01861296	rev/B	C/T	ttcttctcctggacagccggggccaccatt	cactggcttcattcttgctgctcagctgaa	01/30/07	03/31/08	127	Genomic	unknown
ss74807450	AFFY\|SNP_M-178072	fwd/T	A/G	ttcagctgagcagcaagaatgaagccagtg	aatggtggccccggctgtccaggagaagaa	08/09/07	08/09/07	128	Genomic	unknown
ss74885472	ILLUMINA\|ILMN_Human_1M_rs3748140	fwd/T	A/G	ttcagctgagcagcaagaatgaagccagtg	aatggtggccccggctgtccaggagaagaa	08/28/07	08/29/07	129	Genomic	unknown
ss76889558	SI_EXO\|NT_077531.3_1474370	rev/B	C/T	ttcttctcctggacagccggggccaccatt	cactggcttcattcttgctgctcagctgaa	09/20/07	09/20/07	129	Genomic	unknown

Fasta sequence (Legend)

 GTTTGTTTTA ACCTTGAAGC ACCCCCCACC CCCCACCGCA TCTCGTCCCC CCACAACATA
 ATCTTCTCTC AAACGCATGT TGTGCTGGAC CACACCAGAG TTAATCCTGA CCTGTAGCCA
 GGTGGGCATA GATAAAAGGA AATATTGTTT GCCAGTCCCT GCTGGAATGA TGCCTTTACA
 CATCTGTCTG ATCTGATTGC TCCACTGTTT TCTTTCTTCT CTTCCCTTTC CACGGTTCTA
 GCCTGTTCAT CTAGCCCCAT GATGGCTGTG GACATCGAGT ACAGATACAA CTGCATGGCT
 CCTTCCTTGC GCCAAGAGAG GTTTGCCTTT AAGATCTCAC CAAAGCCCAG CAAACCACTG
 AGGCCTTGTA TTCAGCTGAG CAGCAAGAAT GAAGCCAGTG
 R
 AATGGTGGCC CCGGCTGTCC AGGAGAAGAA GGTGAAAAAG CGGGTGTCCT TCGCAGACAA
 CCAGGGGCTG GCCCTGACAA TGGTCAAAGT GTTCTCGGAA TTCGATGACC CGCTAGATAT
 GCCATTCAAC ATCACCGAGC TCCTAGACAA CATTGTGAGC TTGACGACAG CAGAGAGCGA
 GAGCTTTGTT CTGGATTTTT CCCAGCCCTC TGCAGATTAC TTAGACTTTA GAAATCGACT
 TCAGGCCGAC CACGTCTGCC TTGAGAACTG TGTGCTCAAG GACAAGGCCA TTGCAGGCAC
 TGTGAAGGTT CAGAACCTCG CATTTGAGAA GACCGTGAAA ATAAGGATGA CGTTCGACAC
 CTGGAAGAGC TACACAGACT TTCCTTGTCA GTACGTGAAG

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_077531.3

dbSNP Blast Analysis

UniGene Cluster ID
458513

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23953336	AFD_EUR_PANEL	European	48	IG			1.000			1.000

	AFD_AFR_PANEL	African American	46	IG		0.087	0.913	1.000	0.043	0.957

	AFD_CHN_PANEL	Asian	48	IG		0.125	0.875	0.752	0.062	0.938

	HapMap-CEU	European	120	IG		0.033	0.967	1.000	0.017	0.983

	HapMap-HCB	Asian	90	IG		0.067	0.933	1.000	0.033	0.967

	HapMap-JPT	Asian	88	IG		0.045	0.955	1.000	0.023	0.977

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.150	0.833	0.479	0.092	0.908

ss4934163	JBIC-allele		1488	AF					0.094	0.906

ss69038880	HapMap-CEU	European	120	GF		0.033	0.967		0.017	0.983

	HapMap-HCB	Asian	90	GF		0.067	0.933		0.033	0.967

	HapMap-JPT	Asian	90	GF		0.044	0.956		0.022	0.978

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.150	0.833		0.092	0.908

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.080+/-0.183	1263	1052	276	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 .