Reference SNP(refSNP) Cluster Report: rs3771561

Reference SNP(refSNP) Cluster Report: rs3771561

refSNP ID: rs3771561
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/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_014808.1:c.623+868G>A
NT_005416.12:g.1528308G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss91609701 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3771561 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
ss4957621	YUSUKE\|IMS-JST126649	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	08/07/02	10/10/03	107	Genomic	unknown
ss23923668	PERLEGEN\|afd0726536	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	08/10/04	09/13/04	123	Genomic	unknown
ss66241749	AFFY\|SNP_A-4271278	fwd/T	A/G	aaaaggattgaagaac	gtatgggaaagggctc	10/27/06	03/31/08	127	Genomic	unknown
ss66681572	ILLUMINA\|HumanHap300v1.1_rs3771561	fwd/B	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	11/09/06	11/09/06	127	Genomic	unknown
ss67301472	ILLUMINA\|HumanHap550v1.1_rs3771561	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	11/14/06	11/14/06	127	Genomic	unknown
ss67706284	ILLUMINA\|HumanHap650Yv1.0_rs3771561	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	11/14/06	11/14/06	127	Genomic	unknown
ss70780113	ILLUMINA\|HumanHap550v3.0__rs3771561	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	04/20/07	03/30/08	130	Genomic	unknown
ss71356463	ILLUMINA\|HumanHap650Yv3.0_rs3771561	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	04/23/07	04/23/07	127	Genomic	unknown
ss75583428	ILLUMINA\|ILMN_Human_1M_rs3771561	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	08/28/07	08/29/07	129	Genomic	unknown
ss76387463	AFFY\|AFFY_6_1M_SNP_A-4271278	fwd/T	A/G	aaaaggattgaagaac	gtatgggaaagggctc	08/28/07	08/30/07	129	Genomic	unknown
ss79166156	ILLUMINA\|HumanHap300v2.0_rs3771561	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	04/18/07	11/18/07	130	Genomic	unknown
ss84177417	KRIBB_YJKIM\|KHS651198	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	12/04/07	12/06/07	130	Genomic	unknown
ss91609701	BCMHGSC_JDW\|JWB-1407899	fwd/T	A/G	tgctagctaaggggaaaaggattgaagaac	gtatgggaaagggctctgggctctggccca	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 GCAGTGTCTC TGCAGTGTGG CAGAAAGAGT CCTCTACGGG GAAGACACTG TGCTGTGGTA
 GAGGAGGAGG GGACTGTGTG AGGCTAACAG TGTCTGCCTG TGTCAGGGCA TTGGGAATCG
 CCTGGCACCC ATGGCCTTCA TCTCATCTTG TTTTGATTTC TCTAAGACTT GACACTGGTG
 GGTTTTTCTG GATGGAAGTG ATAGAGACCT AGAGAAGGAG TGCTAGCTAA GGGGAAAAGG
 ATTGAAGAAC
 R
 GTATGGGAAA GGGCTCTGGG CTCTGGCCCA GGTGGCTGGG AGCTTTAGTC ACCAAAGGGG
 AGCACTCAGC TGGTGAAAGT GAGTCAGGAG GACTTAGCCT TGCCTTTGTG ACACATCCTG
 TTGAGATGCA GGTTTGTTTG TCAGATCATG TATGTTCATG TGTGTCGTTA AGGCTCTACC
 GGGACCTGCT GGCAGCTGCC CTTTCACACC TTCAAAGTAT GAGTGCCAGC TATGCATCCA
 CCACTGCTGT

GeneView

GeneView via analysis of contig annotation: FARP2 FERM, RhoGEF and pleckstrin domain protein 2

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_005416->NM_014808

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_005416->NM_014808->NP_055623	1528308	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3771561 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838874.1	596755	234109494	plus	G	alt_assembly_8	HuRef	HuRef	view	100
2	NW_921618.1	46937577	236023047	plus	G	alt_assembly_1	Celera	Celera	view	100
2	NT_005416.12	1528308	242002377	plus	G	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005422.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23923668	AFD_EUR_PANEL	European	48	IG	0.042	0.292	0.667	1.000	0.188	0.812

	AFD_AFR_PANEL	African American	46	IG		0.304	0.696	0.403	0.152	0.848

	AFD_CHN_PANEL	Asian	48	IG	0.208	0.500	0.292	1.000	0.458	0.542

	HapMap-CEU	European	120	IG	0.050	0.267	0.683	0.403	0.183	0.817

	HapMap-HCB	Asian	90	IG	0.244	0.489	0.267	1.000	0.489	0.511

	HapMap-JPT	Asian	88	IG	0.182	0.500	0.318	1.000	0.432	0.568

	HapMap-YRI	Sub-Saharan African	118	IG	0.051	0.271	0.678	0.439	0.186	0.814

ss4957621	JBIC-allele		1468	AF					0.393	0.607

ss66241749	HapMap-CEU	European	118	GF	0.051	0.254	0.695		0.178	0.822

	HapMap-HCB	Asian	90	GF	0.244	0.489	0.267		0.489	0.511

	HapMap-JPT	Asian	90	GF	0.178	0.511	0.311		0.433	0.567

	HapMap-YRI	Sub-Saharan African	120	GF	0.050	0.283	0.667		0.192	0.808

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.419+/-0.185	332	260	269	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 .