Reference SNP(refSNP) Cluster Report: rs3802381

Reference SNP(refSNP) Cluster Report: rs3802381

refSNP ID: rs3802381
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:	A/C
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001083536.1:c.243C>A
NM_033086.2:c.243C>A
NP_001077005.1:p.P81P
NP_149077.2:p.P81P
NT_008470.18:g.3059985C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76885646 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3802381 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
ss4988767	YUSUKE\|IMS-JST161074	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	08/12/02	11/22/03	107	Genomic	unknown
ss16240564	CGAP-GAI\|1478255	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	11/18/03	11/22/03	120	cDNA	unknown
ss22880458	SSAHASNP\|WGSA-200403-chr9.chr9.NT_008476.14_3059986	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	03/21/04	03/22/04	121	Genomic	unknown
ss24173912	PERLEGEN\|afd4288657	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	08/10/04	09/13/04	123	Genomic	unknown
ss48401369	APPLERA_GI\|hCV25630355	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	09/28/05	11/03/06	126	Genomic	unknown
ss76885646	SI_EXO\|NT_008470.18_3059986	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	09/20/07	09/20/07	129	Genomic	unknown
ss86344155	CANCER-GENOME\|9982	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	01/25/08	01/25/08	129	Genomic	unknown
ss94106220	BCMHGSC_JDW\|JWB-2621907	fwd/T	A/C	ccccaaccgggacagcgggatcgacagtcc	tcctccagtgtggctggagagaactttccc	02/26/08	03/06/08	129	Genomic	unknown

Fasta sequence (Legend)

 TTCGGTGGGG GGCGGAGGGT ACTGCCTGGG AGCTGCATTT GGGGGTTGCA CCTGAGGGTG
 CTGGTCCATG CCTGGCTAGC ACTGACTCTG GCTTGTTTCT CCCCTACAGG AAGCCCCTGG
 CCAGCCTCCA CCTGAGCCCA GTGAGCTCAG CTTTAAGGAT GGAGTCAGGC AGGGGGTCCT
 CAACCCCTCC AGGACCCATT GCTGCCCTAG GGATGCCAGA CACTGGGCCT GGCAGTTCCT
 CCCTAGGGAA GCTTCAGGCG CTCCCTGTTG GGCCCAGAGC CCACTGTGGG GACCCTGTCA
 GCCTGGCTGC AGCAGGGGAC GGCTCTCCAG ACATAGGCCC CACGGGAGAG CTGAGTGGTA
 GCTTAAAGAT CCCCAACCGG GACAGCGGGA TCGACAGTCC
 M
 TCCTCCAGTG TGGCTGGAGA GAACTTTCCC TGCGAGGAGG GCTTGGAGGC TGGCCCAAGC
 CCCACTGTAC TGGGGGCGCA CGCAGAGATG GCCCTGGACA GCCAGGTCCC GAAGGTCACC
 CCCCAGGAGG AGGCGGACAG CGACGTGGGT GAGGAACCTG ACTCTGAGAA CACCCCCCAG
 AAGGCTGACA AGGATGCCGG CCTGGCCCAG GTAGGCTTCC CCTTCTCTGT CCCCGCTGCG
 GGCTGCAGGC CTTTCCTTAG GAGGGGTTTG AGATTTTCAG TGGGCGTCAT CCCACACCTT
 GTTTCCAGGA ATGTGGCACA CAGGCTCGTG CTGTGTGCAA GGGGAGGTCC TGGGATGCAG
 TCTGCCCTAG AAAAGCCTGA GGGAAAAATC CATGCAGGCC

GeneView

GeneView via analysis of contig annotation: FGD3 FYVE, RhoGEF and PH domain containing 3

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_008470->NM_001083536

function

reference

NT_008470->NM_033086

function

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


reference	NT_008470->NM_001083536->NP_001077005	3059986	forward	871	synonymous	A	Pro [P]	3	81
					contig reference	C	Pro [P]	3	81

reference	NT_008470->NM_033086->NP_149077	3059986	forward	771	synonymous	A	Pro [P]	3	81
					contig reference	C	Pro [P]	3	81

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3802381 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839229.1	1263286	65415938	plus	A	alt_assembly_8	HuRef	HuRef	view	300
9	NW_924484.1	24560625	66180589	plus	A	alt_assembly_1	Celera	Celera	view	300
9	NT_008470.18	3059986	94778602	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008476 BI910798

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_001083536.1 NM_033086.2	AL389924.17

UniGene Cluster ID
411081

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss24173912	AFD_EUR_PANEL	European	48	IG	0.542	0.333	0.125	0.371	0.708	0.292

	AFD_AFR_PANEL	African American	44	IG	0.318	0.500	0.182	1.000	0.568	0.432

	AFD_CHN_PANEL	Asian	44	IG	0.364	0.364	0.273	0.251	0.545	0.455

ss48401369	HapMap-CEU	European	120	IG	1.000				1.000

	AGI_ASP population	multiple	72	IG	0.306	0.500	0.194	1.000	0.556	0.444

ss4988767	JBIC-allele		1498	AF					0.634	0.366

Concordant Genotype	Total Sample	A/A	A/C	C/C
ss24173912	67	28	24	12
ss48401369	124	97	18	7

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C
rs3802381	190	120	42	19

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
188	ss24173912	C/C	PERLEGEN	AFD_EUR_PANEL	NA10851		71_IND_CHR_9
188	ss48401369	A/A	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r23_ch9_CEU_illumina:golden_gate_1.0.0	725881
203	ss24173912	A/C	PERLEGEN	AFD_EUR_PANEL	NA07348		71_IND_CHR_9
203	ss48401369	A/A	CSHL-HAPMAP	HapMap-CEU	NA07348	CEPH1345.02	r23_ch9_CEU_illumina:golden_gate_1.0.0	725881
215	ss24173912	A/C	PERLEGEN	AFD_EUR_PANEL	NA10857		71_IND_CHR_9
215	ss48401369	A/A	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r23_ch9_CEU_illumina:golden_gate_1.0.0	725881
348	ss24173912	A/C	PERLEGEN	AFD_EUR_PANEL	NA10860		71_IND_CHR_9
348	ss48401369	A/A	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r23_ch9_CEU_illumina:golden_gate_1.0.0	725881

Genotype data submitted for	199	samples from	190	individuals	Individual with multiple genotypes submission:	9

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .