Reference SNP(refSNP) Cluster Report: rs1041346

Reference SNP(refSNP) Cluster Report: rs1041346

refSNP ID: rs1041346
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001843.2:c.-76-104315A>G
NM_175038.1:c.-76-104315A>G
NT_029419.11:g.3341150A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1507952 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1041346 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss1507952	TSC-CSHL\|TSC0348210		fwd/T	A/G	gtgctcactaggctaatttatctagttcca	actttactgctactaattgctctagagact	09/07/00	10/25/06	86	Genomic			95 %

Fasta sequence (Legend)

 CCTTGTATGT AATTTGGCTA AGGGTCTGAA TTTCAGAAAA GAAATTTTGG CTAGACATAT
 AAGTTTGAAT TTATTATATA TGATCTTTCA AGTTACAAGA GTAGATGAGA ATATCTAGGG
 AGAGAACATG AAGgagaaga ggagagggga agagggaaga ggagaggaat gatgagaagg
 atacaggaag ggaggagagg agaaggaagg ggaaggagaa gataggggag ATAACTTTTG
 GACCATAGAT CTTTGAGGGA ATATAAAGTG CATCCACTTT AAAGGCATTA AGCTGATCTT
 AATACCTGAT CACTTACACG ACAACAAGCT ATGATTCACT TACAATTACC TACCAAGGGT
 TACTACATGG TGGAGGTAAA GGAGTGGTTG AGTGTGCTCA CTAGGCTAAT TTATCTAGTT
 CCA
 R
 ACTTTACTGC TACTAATTGC TCTAGAGACT ACTGAATGCG GTAATGTGAC TCTCATTAAA
 TGAATAAAAT AATTCCAAGT GACTTGCACT TCTAGACTTT TTTCTGGAAG TTACATAGAA
 CAAAAGACAG ATCAGGTAAA AGCAGTGATT AGGTTGTGGG CTTTGAAATT TCCATCTATT
 CCTTTGAATA TAACAGTAAT AATATTGAAG TAGGAAAGGA GTAACATTTA TAAATGTTAA
 T

GeneView

GeneView via analysis of contig annotation: CNTN1 contactin 1

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_029419->NM_001843

function

reference

NT_029419->NM_175038

function

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


reference	NT_029419->NM_001843->NP_001834	3341150	forward	intron

reference	NT_029419->NM_175038->NP_778203	3341150	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1041346 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838057.1	656400	38224129	plus	A	alt_assembly_8	HuRef	HuRef	view	423
12	NT_029419.11	3341150	39484111	plus	A	ref_assembly	reference	reference	view	423
12	NW_925351.1	3547003	40001097	plus	A	alt_assembly_1	Celera	Celera	view	423

NCBI Resource Links

Submitter-Referenced
GenBank
AC016144.8

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss1507952	HapMap-CEU	European	120	IG	0.933	0.067	1.000	0.967	0.033

	HapMap-HCB	Asian	90	IG	1.000			1.000

	HapMap-JPT	Asian	88	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.019+/-0.095	270	210	0	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 .