Reference SNP(refSNP) Cluster Report: rs885107

Reference SNP(refSNP) Cluster Report: rs885107

refSNP ID: rs885107
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:	C
Clinical Association:	unknown

HGVS Names
NT_010393.15:g.21985798T>C
XM_001717825.1:c.705+65T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1312595 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs885107 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
ss1312595	TSC-CSHL\|TSC0029692	fwd/B	C/T	ctgcttgtaaaagggactgcagcataaagg	cttctgcgtgcagcagacagccttcccttg	09/06/00	04/07/04	86	Genomic	95 %
ss12377026	WI_SSAHASNP\|chr16.NT_024812.10_2072386	fwd/B	C/T	ctgcttgtaaaagggactgcagcataaagg	cttctgcgtgcagcagacagccttcccttg	07/04/03	10/10/03	116	Genomic	unknown
ss43921244	ABI\|hCV7473855	rev/T	A/G	caagggaaggctgtctgctgcacgcagaag	cctttatgctgcagtcccttttacaagcag	07/18/05	11/03/06	126	Genomic	unknown
ss65724246	ILLUMINA\|Human1-rs885107	fwd/B	C/T	ctgcttgtaaaagggactgcagcataaagg	cttctgcgtgcagcagacagccttcccttg	10/10/06	10/10/06	127	Genomic	unknown
ss74857165	ILLUMINA\|ILMN_Human_1M_rs885107	fwd/B	C/T	ctgcttgtaaaagggactgcagcataaagg	cttctgcgtgcagcagacagccttcccttg	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 TGCCTCAGCA GCCGCCTCCC TCACCTCTGG ACTCTGGTCT TCCTCAGGCG TCCTCCCGTC
 ACTCTCTGGA AGCTGGATAC ATAGTAAGTG CTATCCACCT GTCCTGGCCC CTCCCTGCTC
 CACCCTGGGC CTCTTCCCTC TCGTGACACC TCTGTCTTTC CTTCTCCCCA GTGTGACGCG
 GAAAGTGATC TGGACGAGAG GGTGAGTGGG GCTAGAGCTT GGGTGGGCAG TGTCACTGCT
 TGTAAAAGGG ACTGCAGCAT AAAGG
 Y
 CTTCTGCGTG CAGCAGACAG CCTTCCCTTG AGTGAGAAAC ATGGCTTAGG TTGAGTCAGG
 ATTAGGTTTT TGGGAGGAAC GGGGGTGGAT TGGGAGGGTA AATGGCGTCA TTTTTTCTTT
 TGGTGACTAG GGGTTAGCTG ACCCAGGAAT GGAGGGTCCA TGCTTTGGCA TACTATCCCT
 TCCAAAGCCC TTGAGCTACT TCTGGTTCTC CACGGAACCC CAGAGTGGCT GTGGCACTGA
 GATGGGCCCT CTTCCCATCT TAGAATGAAG ACCTAGATCA AGTCTGAGCC GAGACCCGCA
 GATAGAGTTG TGAGGACACT AAATCATTGT AGTCAGTGTA GGGACTAAGC CCTAAAG

GeneView

GeneView via analysis of contig annotation: LOC100129899 hypothetical protein LOC100129899

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_010393->XM_001717825

function

HuRef

NW_001838236->XM_001714827

function

Celera

NW_926306->XM_001715004

function

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


reference	NT_010393->XM_001717825->XP_001717877	21985798	forward	intron

HuRef	NW_001838236->XM_001714827->XP_001714879	354087	forward	intron

Celera	NW_926306->XM_001715004->XP_001715056	1279465	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs885107 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_001838236.1	354087	28235885	plus	T	alt_assembly_8	HuRef	HuRef	view	265
16	NW_926306.1	1279465	29626095	minus	A	alt_assembly_1	Celera	Celera	view	265
16	NT_010393.15	21985798	30580220	plus	T	ref_assembly	reference	reference	view	265

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024812

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1312595	CEPH		184	AF					0.210	0.790

	HapMap-CEU	European	120	IG	0.033	0.417	0.550	0.294	0.242	0.758

	HapMap-HCB	Asian	90	IG		0.111	0.889	0.752	0.056	0.944

	HapMap-JPT	Asian	88	IG	0.023	0.136	0.841	0.251	0.091	0.909

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

ss43921244	AoD_African_American		90	AF					0.800	0.200

	AoD_Caucasian		92	AF					0.340	0.660

	AoD_Chinese		90	AF					0.070	0.930

	AoD_Japanese		90	AF					0.070	0.930

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.475+/-0.110	270	210	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .