Reference SNP(refSNP) Cluster Report: rs4785217

Reference SNP(refSNP) Cluster Report: rs4785217

refSNP ID: rs4785217
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
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_033119.3:c.192+5777A>G
NT_010498.15:g.4203442A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss6602997 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4785217 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
ss6602997	WI_SSAHASNP\|NT_010505.11_2687313	fwd/T	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	02/12/03	04/07/04	111	Genomic	unknown
ss66781699	ILLUMINA\|HumanHap300v1.1_rs4785217	fwd/B	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	11/09/06	11/09/06	127	Genomic	unknown
ss67376183	ILLUMINA\|HumanHap550v1.1_rs4785217	fwd/T	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	11/14/06	11/14/06	127	Genomic	unknown
ss67756479	ILLUMINA\|HumanHap650Yv1.0_rs4785217	fwd/T	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	11/14/06	11/14/06	127	Genomic	unknown
ss70824735	ILLUMINA\|HumanHap550v3.0__rs4785217	rev/B	C/T	aggtaactcagatgtgccaagagccaccaa	gcacgaggctttccacagacagtgccagga	04/20/07	03/31/08	130	Genomic	unknown
ss71406714	ILLUMINA\|HumanHap650Yv3.0_rs4785217	fwd/T	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	04/23/07	04/23/07	127	Genomic	unknown
ss75776323	ILLUMINA\|ILMN_Human_1M_rs4785217	fwd/T	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	08/28/07	08/29/07	129	Genomic	unknown
ss76565901	AFFY\|AFFY_6_1M_SNP_A-8426989	rev/B	C/T	tgccaagagccaccaa	gcacgaggctttccac	08/28/07	08/30/07	130	Genomic	unknown
ss79195187	ILLUMINA\|HumanHap300v2.0_rs4785217	fwd/T	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	04/18/07	11/18/07	130	Genomic	unknown
ss84352136	KRIBB_YJKIM\|KHS691086	fwd/T	A/G	tcctggcactgtctgtggaaagcctcgtgc	ttggtggctcttggcacatctgagttacct	12/04/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 AGGAAGGAGT TGGAGGTGGG GGGAAGAGCT GACCGAGGCC CCAGGCTCAA GCTGCCCTGG
 TAGGATGGGG TTGGGGATTG CCGGGAGGCT TCTGTGTGGA ATCAAGCGGG TAATCAAGAA
 GGGAATGTGG CCTCCAAATG GCTCTGCAGC CTGTGGGAAC TGGAAGTGGT TCCTGGCACT
 GTCTGTGGAA AGCCTCGTGC
 R
 TTGGTGGCTC TTGGCACATC TGAGTTACCT GTCTGTCCCC CTGGACAGGT ATGTTGGGTG
 GAGCAGGGCG GGCAGTCAGC GAGCGTGCTG CCCCTGTGTC ATGGACAGGT CCTTGGGGGC
 TCAACCTGGC CTGTTGGGGT TGGTGGCCCT GCTGTTGTGT TGGGGGAGGA GGTCAGCTGC
 AGGGCTGGAA GCTTAGCTGT

GeneView

GeneView via analysis of contig annotation: NKD1 naked cuticle homolog 1 (Drosophila)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: LOC100130057 hypothetical protein LOC100130057

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_010498->NM_033119

function

reference

NT_010498->XM_001726121

function

HuRef

NW_001838288->XM_001721569

function

Celera

NW_926462->XM_001721852

function

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


reference	NT_010498->NM_033119->NP_149110	4203442	forward	intron

reference	NT_010498->XM_001726121->XP_001726173	4203442	forward	5' near gene

HuRef	NW_001838288->XM_001721569->XP_001721621	683622	reverse	5' near gene

Celera	NW_926462->XM_001721852->XP_001721904	4169349	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4785217 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_926462.1	4169349	35104550	plus	A	alt_assembly_1	Celera	Celera	view	200
16	NW_001838288.2	683622	36477115	minus	T	alt_assembly_8	HuRef	HuRef	view	200
16	NT_010498.15	4203442	49146744	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
11

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
ss6602997	HapMap-CEU	European	120	IG	0.883	0.117		0.655	0.942	0.058

	HapMap-HCB	Asian	90	IG	0.956	0.044		1.000	0.978	0.022

	HapMap-JPT	Asian	90	IG	0.911	0.089		0.752	0.956	0.044

	HapMap-YRI	Sub-Saharan African	120	IG	0.317	0.483	0.200	1.000	0.558	0.442

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.265+/-0.250	270	210	0	0

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 .