Reference SNP(refSNP) Cluster Report: rs5925278

Reference SNP(refSNP) Cluster Report: rs5925278

refSNP ID: rs5925278
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	114/129
Map to Genome Build:	36.3

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

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8202413 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5925278 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
ss8202413	SC_SNP\|NT_011726.8_2684503	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	04/16/03	10/30/04	114	Genomic	unknown
ss24231989	PERLEGEN\|afd3884404	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	08/10/04	09/13/04	123	Genomic	unknown
ss66719190	ILLUMINA\|HumanHap300v1.1_rs5925278	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	11/09/06	11/09/06	127	Genomic	unknown
ss67425939	ILLUMINA\|HumanHap550v1.1_rs5925278	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	11/14/06	11/14/06	127	Genomic	unknown
ss67784581	ILLUMINA\|HumanHap650Yv1.0_rs5925278	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	11/14/06	11/14/06	127	Genomic	unknown
ss69268684	PERLEGEN\|PGP03884404	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	01/30/07	03/31/08	127	Genomic	unknown
ss70849874	ILLUMINA\|HumanHap550v3.0__rs5925278	rev/T	A/G	ttaccaggggatttgtgtgcaccttgaagt	tgctacctgtgccgcacccacacccttttc	04/20/07	03/31/08	130	Genomic	unknown
ss71435019	ILLUMINA\|HumanHap650Yv3.0_rs5925278	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	04/23/07	04/23/07	127	Genomic	unknown
ss75639699	ILLUMINA\|ILMN_Human_1M_rs5925278	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	08/28/07	08/29/07	129	Genomic	unknown
ss77171035	HGSV\|Cor12156_SNV_20070510.chrX_151833848	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	10/09/07	10/11/07	129	Genomic	unknown
ss79211489	ILLUMINA\|HumanHap300v2.0_rs5925278	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	04/18/07	11/18/07	130	Genomic	unknown
ss84431036	KRIBB_YJKIM\|KHS709242	fwd/B	C/T	gaaaagggtgtgggtgcggcacaggtagca	acttcaaggtgcacacaaatcccctggtaa	12/04/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 TTGGAGGGGA GCTGTGGCGT CCCAAGCCCA TGGGTGAAGG GCCGGGTGCA AATCACCCAG
 TGCAACGTAT AGGCCACGTG AGCGCCCTTA TAAACGAGTC ATAGCCCTCG TTTATTTTTT
 ATTGGACTGT TCTAGGGGAG GAGGGCAAAA AATACAGCTA CTGCCTGCAT TTCACAAGGG
 CATTAGTTTT TTTTCGCTGC TCACTGAGAG CCAGATGACT GAAAATATTC CATTCTCCCA
 TTATTCTCCT GATTTCACGA CCAAACATTA CGCACCTAGT ACCCAAACTG CTTCCTGTCG
 TTTCCCAAAG CAGGTTTCTT CCACAGAGGG AAGGTCCTGC GGCTTGCAGC GGCCCGAAAG
 TACTGTTCCA GAAAAGGGTG TGGGTGCGGC ACAGGTAGCA
 Y
 ACTTCAAGGT GCACACAAAT CCCCTGGTAA TCTTAAAAAA ATGCGTGAAG AGATCTGAGG
 CAGGGATGGT TCCACTGAAA GCTAGGTTAC TTGCTGCATA TCCCTGCCCA GGCTGTGTGG
 AGCAAGGGTC TGAAGCCTAT GATTACATTT CAGGGCCAGA AGTTGTGGAC CTTTAGTGAC
 AGAATATATT TGTTTTTCTT TCTCTGTGAT TAAAAAAGAA AAGGCTTTTT CTGGTACTGT
 TTTAATAAAT ATGTTAAAAG CGGACAACAT TTTAAATTTA TGGTCACTGA GAAAGATATT
 TGCAGATATC ACCTTCTTCa gccaggtgtg gtggctcaca cctgtaatcc cagcactttg
 ggaggccaag gtgggcagat cacttgagat cagCCTGGCC

GeneView

GeneView via analysis of contig annotation: LOC100134064 hypothetical protein LOC100134064

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

HuRef

NW_001842415->XM_001714191

function

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


HuRef	NW_001842415->XM_001714191->XP_001714243	110651	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs5925278 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_001842415.2	110651	140963894	minus	A	alt_assembly_8	HuRef	HuRef	view	400
X	NT_011726.13	3081216	151913936	plus	C	ref_assembly	reference	reference	view	400
X	NW_927732.1	205083	152497436	plus	C	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011726

dbSNP Blast Analysis
GenBank HTGS Finished:
NC_000023.9 U82671.5

Population Diversity

	Sample Ascertainment				Genotype Detail						Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C	C/C	C/T	T	T/T	HWP	C	T
ss24231989	AFD_EUR_PANEL	European	48	IG		0.583	0.167		0.250	0.003	0.667	0.333

	AFD_AFR_PANEL	African American	46	IG		0.826	0.087		0.087	0.005	0.870	0.130

	AFD_CHN_PANEL	Asian	46	IG		0.478	0.217		0.304	0.010	0.587	0.413

ss69268684	HapMap-CEU	European	90	IG		0.267	0.233			0.527	0.733	0.267

	HapMap-HCB	Asian	68	IG		0.111	0.222		0.178	0.294	0.500	0.500

	HapMap-JPT	Asian	65	IG		0.256	0.186		0.070	0.317	0.631	0.369

	HapMap-YRI	Sub-Saharan African	90	IG		0.300	0.167		0.033	0.584	0.789	0.211

ss8202413	HapMap-CEU	European	120	IG		0.600	0.233		0.167	0.527	0.717	0.283

	HapMap-HCB	Asian	88	IG		0.432	0.227		0.341	0.371	0.545	0.455

	HapMap-JPT	Asian	88	IG		0.477	0.182		0.341	0.200	0.568	0.432

	HapMap-YRI	Sub-Saharan African	120	IG		0.717	0.183		0.100	0.584	0.808	0.192

	CHMJ	Asian	74	IG	0.622			0.378			0.622	0.378

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24231989	71	26	11	9
ss69268684	268	66	48	12
ss8202413	268	161	47	58

RefSNP Genotype Summary	Total Individual	C	C/C	C/T	T	T/T
rs5925278	332		183	59		66

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5181	ss8202413	C/T	CSHL-HAPMAP	HapMap-HCB	NA18576	CH18576	r23_chX_HCB_illumina:golden_gate_1.1.0	1011593
5181	ss69268684	T/T	CSHL-HAPMAP	HapMap-HCB	NA18576	CH18576	chrX-HapMap-HCB
5260	ss8202413	C/T	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r23_chX_YRI_illumina:golden_gate_1.1.0	1011593
5260	ss69268684	T/T	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	chrX-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .