Reference SNP(refSNP) Cluster Report: rs2049234

Reference SNP(refSNP) Cluster Report: rs2049234

refSNP ID: rs2049234
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	94/129
Map to Genome Build:	36.3

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

HGVS Names
NM_017861.2:c.195+2524C>T
NT_029928.12:g.1071685C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss42121072 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2049234 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
ss2959420	TSC-CSHL\|TSC1069555	fwd/T	A/G	ttaataaccctacctaaaaaagtgaaatga	gtttatttgatctgccttatccttggtgaa	01/29/01	10/10/03	94	Genomic	unknown
ss23706854	PERLEGEN\|afd4029972	rev/B	C/T	ttcaccaaggataaggcagatcaaataaac	tcatttcacttttttaggtagggttattaa	08/10/04	08/20/04	123	Genomic	unknown
ss42121072	ABI\|hCV11975026	rev/B	C/T	ttcaccaaggataaggcagatcaaataaac	tcatttcacttttttaggtagggttattaa	07/17/05	07/17/05	126	Genomic	unknown

Fasta sequence (Legend)

 TCTCTGCCCT TCATTGCCTG ATATTCAATG ACTTTTTTCA TTATTTCATA TATTTTGTCT
 ATTTCTTGCT TGTTTCAAGT AAGAGACTAA ATTTGTTACC TGTTCTCCAC TTGACCAGAA
 GCAGAAGCCT TAATACTACA TACTTTGAGT AAAACTTATG GTTTCAAAAA CTGTTTCCAT
 TTTGACCCAC AAAACAGCAA TTTTATACGT TTCAATCTAA TATTATACTG CTTTCAAAGA
 ATCTAAGAGA CTTCTGATGA AAAAATATGT TTAATAACCC TACCTAAAAA AGTGAAATGA
 R
 GTTTATTTGA TCTGCCTTAT CCTTGGTGAA CCTACTTAAG GCTTGCATTT ATTTTCAAAT
 TATTCACAAA CCATCACAAA CTCCTTACAA AGCATTTTGC TGGCACACCA CTCATTTAAT
 CTGGGCCCAC AGTTCCATTT GTTGCAGCCA AAAATTTTAT TTCCTGGAGC AGAGTCAAGA
 CATTAATCCA GGTATACAAG CATCAATCAG TCCCTACATA TAAATTCCTT CTACCCAGTT
 ACACTTATTA TATAATAACA CTTAGCATAA CAAAGTTTCT CTGTACGAGG AATTGGGCCA

GeneView

GeneView via analysis of contig annotation: PIGX phosphatidylinositol glycan anchor biosynthesis, class X

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_029928->NM_017861

function

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


reference	NT_029928->NM_017861->NP_060331	1071685	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2049234 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_001838889.1	780391	193748640	minus	C	alt_assembly_8	HuRef	HuRef	view	300
3	NW_921873.1	713968	195032488	minus	C	alt_assembly_1	Celera	Celera	view	300
3	NT_029928.12	1071685	197936348	minus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000003.6

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss23706854	AFD_EUR_PANEL	European	48	IG		1.000			1.000

	AFD_AFR_PANEL	African American	46	IG	0.043	0.957	1.000	0.022	0.978

	AFD_CHN_PANEL	Asian	48	IG		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.014+/-0.082	71	50	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 .