Reference SNP(refSNP) Cluster Report: rs42889

Reference SNP(refSNP) Cluster Report: rs42889

refSNP ID: rs42889
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002294.1:c.1093+4044A>G
NM_013995.1:c.*1468A>G
NT_011786.15:g.3839251T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8183774 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs42889 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
ss48752	KWOK\|OVLP-87226	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	04/28/00	04/07/04	76	Genomic	83 %
ss8183774	SC_SNP\|NT_011588.11_3769731	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	04/16/03	05/16/04	114	Genomic	unknown
ss8551495	SC_SNP\|NT_077819.2_3831484	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	05/23/03	10/10/03	116	Genomic	unknown
ss10574262	BCM_SSAHASNP\|chrX.NT_077819.2_3831484	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	06/29/03	10/10/03	116	Genomic	unknown
ss12052044	WI_SSAHASNP\|chrX.NT_077819.2_3831484	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	07/04/03	10/10/03	116	Genomic	unknown
ss20991947	SSAHASNP\|WGSA-200403-chrX.chrX.NT_077819.3_3839251	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	03/19/04	03/19/04	121	Genomic	unknown
ss43563940	ABI\|hCV2256951	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	07/18/05	11/03/06	126	Genomic	unknown
ss65746819	ILLUMINA\|Human1-rs42889	fwd/T	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	10/10/06	10/10/06	127	Genomic	unknown
ss71649224	SI_EXO\|NT_011786.15_3839251	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	05/07/07	05/07/07	127	Genomic	unknown
ss74870156	ILLUMINA\|ILMN_Human_1M_rs42889	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	08/28/07	08/29/07	129	Genomic	unknown
ss84046400	HGSV\|Cor19240_SNV_20070510.chrX_119353423	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	11/30/07	12/06/07	130	Genomic	unknown
ss94385720	BCMHGSC_JDW\|JWB-2701894	fwd/B	C/T	gcacgtgaattaaaaatgattctaccataa	gaataataacaacgaaagttttgattagca	02/26/08	03/06/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGCCtatata tgtgtgcata tatatatata tgtctgtgtg tgtgtatTGA TCCATTCAAT
 GTCAATATTT TGGAACCCAG ACAATTTTCT CATTTTCTAG TGAATGGGAG GCACATAATC
 CCACCACAAA AAAAAAAAAA ACACGAAAAA ACAACCCCAC AGGAACCTTC CATATATGGC
 TGCATATTAA CAATTTTAAT ATTTGCTCAG CCATTCCAAC ACACACCAAA AAAGTTCTCC
 TAGAAGCAGC AAGAAATATT TGATGTGTTA ACTACCAAGC TGATGTATTT TGCTTTCTCC
 TATAAACATT AGGTGGTACA CGGTAATTTG ACAATTGGTA CATCTCTCAG ACCACAAAAC
 TGAACACAAA GCACGTGAAT TAAAAATGAT TCTACCATAA
 Y
 GAATAATAAC AACGAAAGTT TTGATTAGCA CAGAACCATT TAAATGTGAA AGCCAAATTA
 GTGATGTTGT AGCAATCAAT GCAAGCTGGA AACAAAGAAC AACTTTTTAA TGGATTAAGA
 TAAAACCAAG ACTTTTTGGT TAGATGCAAG ttttgtttgt ttgtttgttt tgttttgttt
 tgttttgaga tggagtttcg tttttgtcgc ccaggctgga gtgcaatggt gcgctcttgg
 ctcaccgcaa cctctgcctc ccgggttcaa gtgattctcc tgcctcagcc tcccgagtaa
 ctgggattac aggcgcccac caccacgccc agctaatttt ttgtatttct gatagagatg
 gggtttcacc atgttggcca ggctggtctc aaactcctgG

GeneView

GeneView via analysis of contig annotation: LAMP2 lysosomal-associated membrane protein 2

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_011786->NM_002294

function

reference

NT_011786->NM_013995

function

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


reference	NT_011786->NM_002294->NP_002285	3839251	reverse		intron

reference	NT_011786->NM_013995->	3839251	reverse	2838	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs42889 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_001842396.2	183413	109022638	minus	G	alt_assembly_8	HuRef	HuRef	view	400
X	NT_011786.15	3839251	119455569	plus	T	ref_assembly	reference	reference	view	400
X	NW_927721.1	241934	120036359	plus	T	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077819

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_013995.1

UniGene Cluster ID
496684

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss43563940	AoD_African_American		90	AF					0.950	0.050

	AoD_Caucasian		92	AF					0.630	0.370

	AoD_Chinese		90	AF					0.780	0.220

	AoD_Japanese		90	AF					0.900	0.100

ss48752	SC_12_A	Asian	14	IG	0.286			0.010	0.857	0.143

	SC_12_C	European	14	IG	0.429	0.143		0.150	0.786	0.214

ss8183774	HapMap-CEU	European	120	IG	0.483	0.250	0.267	0.294	0.608	0.392

	HapMap-HCB	Asian	90	IG	0.778	0.133	0.089	1.000	0.844	0.156

	HapMap-JPT	Asian	88	IG	0.864	0.114	0.023	0.479	0.920	0.080

	HapMap-YRI	Sub-Saharan African	120	IG	0.967	0.017	0.017	1.000	0.975	0.025

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.279+/-0.248	292	223	2	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .