Reference SNP(refSNP) Cluster Report: rs12690163

Reference SNP(refSNP) Cluster Report: rs12690163

refSNP ID: rs12690163
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NG_007091.1:g.17366G>C
NM_000047.2:c.430+1238G>C
NT_011757.15:g.751708C>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss20397720 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12690163 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
ss20397720	CSHL-HAPMAP\|CSHL-HuFF-200402.chrX.NT_025302.12_551633		fwd/T	C/G	ttttttttttttttttggtaaaaaattaaa	aaagaacattttataatttttaatttttag	02/21/04	03/04/04	120	Genomic			unknown
ss21054195	SSAHASNP\|WGSA-200403-chrX.chrX.NT_025302.12_551633		fwd/T	C/G	ttttttttttttttttggtaaaaaattaaa	aaagaacattttataatttttaatttttag	03/19/04	03/19/04	121	Genomic			unknown

Fasta sequence (Legend)

 CCAATGCTGT CTGCCATCTG GAAAACCTCA TGATTTCCCA ATGGATATCC CTTAAGGATA
 GACTCTTCTG TCTTAGAAAA ATTATAGTTg gccaggcatg gtggttcaca actataatcc
 cagcactttg ggaggccgag gtgagaggat tccttgtgcc caggattgct ggagaccagc
 ctgggtagca tgggaagacc ccatctctac aaaaaaaaaa aaaaaaaaaa agaaaaaaaa
 gaaaaaatta accgggcatg gtggtgcaag cctgtagtac caactgcttg ggagactaag
 gtgggaggat cacttgagtc tgggaggtcg agactgcagt gagctgtgac tgcaccattg
 ccctctagcc tgagtaacag agtgagtacc ctgtttaaaa aaaaaaaaaa aGTCTATTGG
 AAAAAATACA CCTTTGTTTG ACAGCGATGA CTGAATCTCC CCAGAATTTG tttttttttt
 ttttttggta aaaaattaaa
 S
 aaagaacatt ttataatttt taatttttag aaatatagtt tattgaattt tataCTCATT
 GTATCCACTA GTCATGTTGT TTGTTATCAA TAAATGGAAC TGTTGATAAC AATCATTACT
 ATAACACAAT AATGATAATG GCAACTTGGT CTCCTCTCAA GGAACTGTTG TCATTAATTT
 TATTTTTCAT CCAATACATG ACATGTTTGT TGACTTGTAG AAAAATAACC ATGTTAGTTA
 TGGAAGCTGA CAGG

GeneView

GeneView via analysis of contig annotation: ARSE arylsulfatase E (chondrodysplasia punctata 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_011757->NM_000047

function

HuRef

NW_001842356->NM_000047

function

Celera

NW_927700->NM_000047

function

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


reference	NT_011757->NM_000047->NP_000038	751708	reverse	intron

HuRef	NW_001842356->NM_000047->NP_000038	813338	reverse	intron

Celera	NW_927700->NM_000047->NP_000038	1548454	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12690163 maps exactly once on NCBI human chromosome X

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
X	NW_001842356.1	813338	813338	plus	C	alt_assembly_8	HuRef	HuRef	view	500
X	NT_011757.15	751708	2879946	plus	C	ref_assembly	reference	reference	view	500
X	NW_927700.1	1548454	7150172	plus	C	alt_assembly_1	Celera	Celera	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_025302

dbSNP Blast Analysis
GenBank HTGS Finished:
AC005295.1 NC_000023.9

Population Diversity

There is no frequency data.

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 .