Reference SNP(refSNP) Cluster Report: rs1055114

Reference SNP(refSNP) Cluster Report: rs1055114

refSNP ID: rs1055114
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_178815.3:c.*2596T>C
NT_008705.15:g.942066T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52067677 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1055114 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
ss1533584	LEE\|606789	fwd/B	C/T	attatttcagtgatgaaataatttgtgttt	atatcccccttcacctccatgtattggtta	09/13/00	05/16/04	86	cDNA	unknown
ss4396797	LEE\|ge606789	fwd/B	C/T	attatttcagtgatgaaataatttgtgttt	atatcccccttcacctccatgtattggtta	04/25/02	10/10/03	106	cDNA	unknown
ss4422408	LEE\|e606789	fwd/B	C/T	attatttcagtgatgaaataatttgtgttt	atatcccccttcacctccatgtattggtta	04/26/02	10/10/03	106	cDNA	unknown
ss52067677	SI_EXO\|NT_008705.15_942066	fwd/B	C/T	attatttcagtgatgaaataatttgtgttt	atatcccccttcacctccatgtattggtta	03/29/06	03/29/06	127	Genomic	unknown
ss69359633	RSG_JCVI\|ARL5B-021407_021408-C_T	fwd/B	C/T	attatttcagtgatgaaataatttgtgttt	atatcccccttcacctccatgtattggtta	03/21/07	08/14/07	127	Genomic	unknown

Fasta sequence (Legend)

 TTTGGATTAG AAATGATTTA TGTTAGCCAT GTGTTGAAGA TGAAATTGGC ATCAGTGTAG
 ACGGTGCTGA TTGGGAAAAG TTCATGATTA GGAAATTCAT GTAAGACTTT TTAAGAGTAT
 TTTTTAGGTT TTCACTCAAT CTTTCCTGTC ACAGTAACGT GAAAACTGAT TATTCTTTAC
 TCCAAGAGAA TGTTTTAACC CAAGCAAGTA TCTAATACTA GAGCATTGGT TCTGACATTC
 ATTGTAAATC AGTGAACTGT AAGATACTGT CTAAAAAATG TACATTTGTA ATTAGTGCCT
 TTATTCATAT TTTGAAATAA GTTCTTAGTT TTATATTATA CCTGTTCTTT AGAAGTCATG
 TTAGCAGCTA ATTATTTCAG TGATGAAATA ATTTGTGTTT
 Y
 ATATCCCCCT TCACCTCCAT GTATTGGTTA GCACAGTTTA TAGTAAGTGA AAAGCAAGGG
 ACCCACCTAC ATTACCTTCA GGAGACTGTT CTACCTTTTA ATTTGAAAAC AAGGAAATTA
 AATTTTAACA GAAATCTTTT AAGTATGTTA TAACCAAAGT GTTCAATTAT CCTTGCAAGT
 TCAAATACAG CATTTTTCTT AATTTTGAGC GTGTCATGTC CTTCATCTTT AAACCCATCA
 TTCTTATTGA AGCCCATTTG AGAACTCTTA GAATTAATAG AACCTTTTAT AAGGGAATAT
 ATGGAATATT TTTTATTGTT AATGTAACTT AATTCCTTAA AACCTGGAAT ATTAATATAT
 ATAATCTATT AAAAGCTGAA GATTAAATAT GTAATTTTTG

GeneView

GeneView via analysis of contig annotation: ARL5B ADP-ribosylation factor-like 5B

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_008705->NM_178815

function

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


reference	NT_008705->NM_178815->	942066	forward	3390	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1055114 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_001837931.2	12154789	18627188	minus	A	alt_assembly_8	HuRef	HuRef	view	400
10	NW_924584.1	18652258	18652258	plus	T	alt_assembly_1	Celera	Celera	view	400
10	NT_008705.15	942066	19006747	plus	T	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008705.15 Hs.127221

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_178815.3	AL512641.9

UniGene Cluster ID
25362

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	C	T
ss1533584	CEPH		184	AF		0.770	0.230

ss69359633	R12_ISDP2		40	AF		0.075	0.925

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.457+/-0.140	0	0	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .