Reference SNP(refSNP) Cluster Report: rs624834

Reference SNP(refSNP) Cluster Report: rs624834

refSNP ID: rs624834
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_178124.3:c.-97C>T
NT_011681.15:g.5069874C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss797298 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs624834 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
ss797298	SC_JCM\|AF011889.1_312174		fwd/B	C/T	ccatgggatggacctgagtcagccgaatcc	agccccttcccttgggcctgctgtggtgct	07/27/00	10/10/03	83	Genomic			unknown

Fasta sequence (Legend)

 AAGAGGGCTA ACACCAGCCC GGACTCTCCA CTCTGGCTAG GCCAAGGGGG CCCTCTGTCC
 TCTGTGTTGC CCTAGGGCTC GGTGACCTCT GTCATAGCAC TGACCACATG GTATCCTGCC
 TGTGCCTTCC TCTAGCTGTC CCCGCCCTAC TCCGGACCGC CCCAAAGACT CCATGGGATG
 GACCTGAGTC AGCCGAATCC
 Y
 AGCCCCTTCC CTTGGGCCTG CTGTGGTGCT GGACATCAGT GACAGACGGA AGCAGGAGAC
 CATCAAGGTC AGTGCGATTT AGGCCACCTG AGAGACACGG GGGGAAGGTC AGGCCACTGC
 CCATGAGCTT GGAGGGCTGG CGTGTGATGC GCTTCTGTGC TTCCGCAGGC TACGGGAGGC
 CCGGGGCGCT TGCGAAGATG

GeneView

GeneView via analysis of contig annotation: CXorf40A chromosome X open reading frame 40A

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_011681->NM_178124

function

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


reference	NT_011681->NM_178124->	5069874	forward	446	5' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs624834 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_001842412.2	100061	137580381	minus	A	alt_assembly_8	HuRef	HuRef	view	200
X	NT_011681.15	5069874	148434884	plus	C	ref_assembly	reference	reference	view	200
X	NW_927727.1	2723760	148975697	plus	T	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AF011889 U66083

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_178124.3	AF011889.1

UniGene Cluster ID
425383

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	C	T
ss797298	CEPH		184	AF		1.000

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

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Revised: May 25, 2006 1:38 PM .