Reference SNP(refSNP) Cluster Report: rs241938

Reference SNP(refSNP) Cluster Report: rs241938

refSNP ID: rs241938
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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
NT_011109.15:g.10578499A>G
XM_932239.3:c.557+24A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss311467 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs241938 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
ss311467	KWOK\|OVLP-000621-378195	rev/B	C/T	tgttagcagggaggtttctggccactgtat	attttggtgaggcagatgtagacctgagat	06/30/00	10/25/06	79	Genomic	97 %
ss1246022	KWOK\|OVLP-000804-480291	fwd/T	A/G	atctcaggtctacatctgcctcaccaaaat	atacagtggccagaaacctccctgctaaca	09/02/00	10/10/03	86	Genomic	97 %
ss2462357	SC_JCM\|AC007676.19_149754	fwd/T	A/G	atctcaggtctacatctgcctcaccaaaat	atacagtggccagaaacctccctgctaaca	11/03/00	10/10/03	89	Genomic	unknown
ss66313081	AFFY\|SNP_A-1876958	fwd/T	A/G	tctgcctcaccaaaat	atacagtggccagaaa	10/29/06	08/14/07	127	Genomic	unknown
ss67651250	ILLUMINA\|HumanHap650Yv1.0_rs241938	fwd/T	A/G	atctcaggtctacatctgcctcaccaaaat	atacagtggccagaaacctccctgctaaca	11/14/06	11/14/06	127	Genomic	unknown
ss71301169	ILLUMINA\|HumanHap650Yv3.0_rs241938	fwd/T	A/G	atctcaggtctacatctgcctcaccaaaat	atacagtggccagaaacctccctgctaaca	04/23/07	04/23/07	127	Genomic	unknown
ss75379244	ILLUMINA\|ILMN_Human_1M_rs241938	fwd/T	A/G	atctcaggtctacatctgcctcaccaaaat	atacagtggccagaaacctccctgctaaca	08/28/07	08/29/07	129	Genomic	unknown
ss75994907	AFFY\|AFFY_6_1M_SNP_A-1876958	fwd/T	A/G	tctgcctcaccaaaat	atacagtggccagaaa	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GTGGGCCTTC AATCTTCTAA GATGGGAATA GAAAGAAGAG GATCTACCCA GACCAGGACC
 CTGCTGCCCA ATCTCAGGTC TACATCTGCC TCACCAAAAT
 R
 ATACAGTGGC CAGAAACCTC CCTGCTAACA TCATAGTTTG TCTGTGATGC AGAAATGCCT
 CTGttttgtt gttgttttgt ttttgtagag acagggtctt gctctgtcac ctaggttgga
 gtgcactggc acaatcatag ttcactgcag ccttgaactc ctggactcaa gcgatcctac
 cgcctcagcc tcccaagtag ctgggattat aggcatgcgc catcatgcct agctgatttt
 tattttgtag agactgggtc tcactatgtt gcccaggctg gccttgaact cttgacctca
 agcgatcttc ctgcctcagc ctccccagtt gctgggatta caggcgtgag ccatcgtgcc
 tggccCCAGA AATGCTTCGC TTCTATGACT TTGTTCAGTG GAGACCTCTG TGATT

GeneView

GeneView via analysis of contig annotation: LOC644554 hypothetical LOC644554

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_011109->XM_932239

function

HuRef

NW_001838496->XM_001717378

function

Celera

NW_927217->XM_944596

function

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


reference	NT_011109->XM_932239->XP_937332	10578499	forward	intron

HuRef	NW_001838496->XM_001717378->XP_001717430	526311	forward	intron

Celera	NW_927217->XM_944596->XP_949689	517399	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs241938 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838496.1	526311	34759937	plus	A	alt_assembly_8	HuRef	HuRef	view	100
19	NW_927217.1	517399	35110628	plus	A	alt_assembly_1	Celera	Celera	view	100
19	NT_011109.15	10578499	43002121	plus	A	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
AC007676.19 AC016582 AC016582.5

dbSNP Blast Analysis

UniGene Cluster ID
531262

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss311467	HapMap-CEU	European	118	IG	1.000			1.000

	HapMap-HCB	Asian	86	IG	1.000			1.000

	HapMap-JPT	Asian	90	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	0.881	0.119	0.655	0.941	0.059

ss66313081	HapMap-CEU	European	118	GF	1.000			1.000

	HapMap-HCB	Asian	90	GF	1.000			1.000

	HapMap-JPT	Asian	90	GF	1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.883	0.117		0.942	0.058

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.033+/-0.124	270	210	269	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 .