Reference SNP(refSNP) Cluster Report: rs3816100

Reference SNP(refSNP) Cluster Report: rs3816100

refSNP ID: rs3816100
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:	C/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_173075.2:c.2043+144G>C
NT_006238.10:g.525710C>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss92543591 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3816100 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
ss5002512	YUSUKE\|IMS-JST176495	fwd/T	C/G	atgctttactttataacgccgtcattccta	ggccagaatcagttatgataaacagattac	08/12/02	10/10/03	107	Genomic	unknown
ss24654273	PERLEGEN\|afd3462900	rev/B	C/G	gtaatctgtttatcataactgattctggcc	taggaatgacggcgttataaagtaaagcat	08/10/04	09/13/04	123	Genomic	unknown
ss68897330	PERLEGEN\|PGP03462900	rev/	C/G	gtaatctgtttatcataactgattctggcc	taggaatgacggcgttataaagtaaagcat	01/30/07	03/31/08	127	Genomic	unknown
ss92543591	BCMHGSC_JDW\|JWB-1766141	rev/	C/G	gtaatctgtttatcataactgattctggcc	taggaatgacggcgttataaagtaaagcat	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 CATTTGCCTT CATCATGGAC ACGGGGAACC AGCGCTTTGA GTGCCACGTT TTCTGGTGCG
 AGCCTAATGC TGGTAACGTG TCTGAGGCGG TGCAGGCCGC CTGCATGGTG AGTTATCCCG
 GTACAGGCTG TTGAGCCCTC CCGCCTCTGC TCATCTCTAA TATGCCATAC ATTATAGCAG
 AATCACTCAC GGAAATGAAA AAAGTCGAAT CCCTAAAGTA ATGCTTTACT TTATAACGCC
 GTCATTCCTA
 S
 GGCCAGAATC AGTTATGATA AACAGATTAC ATCTCCAAAG GCCAGAACTC CTGAAAGAAG
 TGGGGCCAGA TAGAGGCTCC GATGAGTTTC ATAACCACCA CCTTGACGAC GGTCAATCCT
 TGATCCCAAA TCAATTTCAT GTGTGAAATG TTGGTCGTGT ATGAGTTGGT ACTGTTTGGG
 TTCAATTCAG TACTTTAAAA ATCAATACAT TGAATGACTT TTGTTTCCAG TGATTGGTTT
 CTGTACACCG

GeneView

GeneView via analysis of contig annotation: APBB2 amyloid beta (A4) precursor protein-binding, family B, member 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_006238->NM_173075

function

HuRef

NW_001838903->NM_173075

function

Celera

NW_922073->NM_173075

function

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


reference	NT_006238->NM_173075->NP_775098	525710	reverse	intron

HuRef	NW_001838903->NM_173075->NP_775098	524148	reverse	intron

Celera	NW_922073->NM_173075->NP_775098	31393806	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3816100 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838903.1	524148	40145713	minus	C	alt_assembly_8	HuRef	HuRef	view	100
4	NT_006238.10	525710	40518501	minus	C	ref_assembly	reference	reference	view	100
4	NW_922073.1	31393806	41267064	minus	C	alt_assembly_1	Celera	Celera	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000004.9

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss24654273	AFD_EUR_PANEL	European	48	IG	0.125	0.458	0.417	1.000	0.354	0.646

	AFD_AFR_PANEL	African American	46	IG	0.130	0.304	0.565	0.251	0.283	0.717

	AFD_CHN_PANEL	Asian	48	IG		0.125	0.875	0.752	0.062	0.938

	HapMap-CEU	European	116	IG	0.121	0.483	0.397	0.752	0.362	0.638

	HapMap-HCB	Asian	88	IG	0.045	0.273	0.682	0.584	0.182	0.818

	HapMap-JPT	Asian	90	IG	0.022	0.178	0.800	0.527	0.111	0.889

	HapMap-YRI	Sub-Saharan African	118	IG	0.169	0.305	0.525	0.025	0.322	0.678

	CHMJ	Asian	74	IG					0.243	0.757

ss5002512	JBIC-allele		1496	AF					0.181	0.819

ss68897330	HapMap-CEU	European	120	GF	0.117	0.483	0.400		0.358	0.642

	HapMap-HCB	Asian	90	GF	0.044	0.267	0.689		0.178	0.822

	HapMap-JPT	Asian	90	GF	0.022	0.178	0.800		0.111	0.889

	HapMap-YRI	Sub-Saharan African	120	GF	0.183	0.300	0.517		0.333	0.667

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.380+/-0.214	332	260	270	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 .