Reference SNP(refSNP) Cluster Report: rs1299525

Reference SNP(refSNP) Cluster Report: rs1299525

refSNP ID: rs1299525
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
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
NM_001908.3:c.-26+3385G>A
NM_147780.2:c.-187-153G>A
NM_147781.2:c.-144-3137G>A
NM_147782.2:c.-113-153G>A
NM_147783.2:c.-99-3137G>A
NT_077531.3:g.4197475C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2073589 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1299525 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
ss2073589	KWOK\|OVLP-000925-551866	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	10/07/00	10/25/06	87	Genomic	85 %
ss2524257	SC_JCM\|AC025857.2_101036	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	11/03/00	10/10/03	110	Genomic	unknown
ss10429223	BCM_SSAHASNP\|chr8.NT_077531.2_4032157	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	06/29/03	10/10/03	116	Genomic	unknown
ss14333296	WI_SSAHASNP\|chr8.NT_077531.3_4197475	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	11/05/03	11/22/03	119	Genomic	unknown
ss17205643	CSHL-HAPMAP\|CSHL-HuAA-200402.chr8.NT_077531.3_4197475	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	02/17/04	03/04/04	120	Genomic	unknown
ss23378697	PERLEGEN\|afd1864972	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	08/10/04	09/13/04	123	Genomic	unknown
ss44914093	ABI\|hCV8339781	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	07/19/05	07/19/05	126	Genomic	unknown
ss67051220	ILLUMINA\|HumanHap550v1.1_rs1299525	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	11/14/06	11/14/06	127	Genomic	unknown
ss67377444	ILLUMINA\|HumanHap650Yv1.0_rs1299525	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	11/14/06	11/14/06	127	Genomic	unknown
ss68142817	ILLUMINA\|HumanHap250Sv1.0_rs1299525	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	12/06/06	12/07/06	127	Genomic	unknown
ss69039968	PERLEGEN\|PGP01864972	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	01/30/07	08/14/07	127	Genomic	unknown
ss70590931	ILLUMINA\|HumanHap550v3.0__rs1299525	rev/T	A/G	ttttagtttcaagccttatcgtccgcctct	tagaccactcctgtgcctgtttcctgatcc	04/20/07	03/30/08	130	Genomic	unknown
ss71134590	ILLUMINA\|HumanHap650Yv3.0_rs1299525	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	04/23/07	04/23/07	127	Genomic	unknown
ss75655051	ILLUMINA\|ILMN_Human_1M_rs1299525	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	08/28/07	08/29/07	129	Genomic	unknown
ss76844998	AFFY\|AFFY_6_1M_SNP_A-8706606	fwd/B	C/T	gcacaggagtggtcta	agaggcggacgataag	08/28/07	08/30/07	129	Genomic	unknown
ss83715024	KRIBB_YJKIM\|KHS526081	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	12/04/07	12/05/07	130	Genomic	unknown
ss84549758	HGSV\|Cor18517_SNV_20070510.chr8_11759534	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	12/06/07	12/07/07	130	Genomic	unknown
ss93833168	BCMHGSC_JDW\|JWB-2424381	fwd/B	C/T	ggatcaggaaacaggcacaggagtggtcta	agaggcggacgataaggcttgaaactaaaa	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATCCATGTAG TGTAACTGAA GTCATATAAA CTTTAATAAC ATTGTTTATA CACTGATGCA
 GAGTTTTAAA AGTACAAAAA GGCCTGGAgg tgactcatgc cttgtaatcc cagcatttgg
 aaggcctaag tgggaggagg caaggggatc acttgaaacc aggagtttca gagcagtcct
 ggcaacagtg agaccctgtc tctacaaacg aaaaaaaaaa aaaaaaaaaa aaaaacctgg
 gcaccgcctg tggtcccagc tacttactac tcgggaggct gaggtgggaa ccagatcgct
 tacatctggg tggctgaggc tgccgtgagc cgtggtcgca ccactgcaca ccagcctggg
 agacaaagca agaccctgtc ATTAATCAAA CAATAAATGA ATGAATGCAT GAACAAAAAA
 ATGTGCAGGA GAATCCAAAA GAGGGGCAGC AGACAGGGAA TACAATGGCC CTTGGAAGGA
 TCAGGAAACA GGCACAGGAG TGGTCTA
 Y
 AGAGGCGGAC GATAAGGCTT GAAACTAAAA AAGAGATTAG TTAAAAGTCT AAACACATgg
 ctgggcacag tgactcacac ctgtaatccc aacactttgg gaggcgaggc gggcagatca
 tttgaggtct ctactaaaaa tacaaaaatt agccaggcat ggtggtgcat gcctctaatc
 ccagctactc cggaggctga ggcaggaaca ttgcttgaac ctgggaggta aggttgcagt
 gagctgagat tgtgccacgg cattccagcc tgggtgacag agtgaaactc tgtctcaaaa
 aaaaaaagaa agaaaaAAAT GTCTAAACAC AGAGTGGAAT TTGATCCCTA AACCTCCTAC
 CCCACACAAG CTagggtaaa tataaacatt aacaaccatg ccagggcgca aggtttgcct
 cccacatgct ctttctcagg cagcctggGA CCAGACGTAG AGACTGCTGC CTGCCACCCT
 GATATCCCAG AGGCACAGCA CATCTGTACA TGCCTCCCCT AGACTCAACT GCCTGTCACC
 CCAA

GeneView

GeneView via analysis of contig annotation: CTSB cathepsin B

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_077531->NM_001908

function

reference

NT_077531->NM_147780

function

reference

NT_077531->NM_147781

function

reference

NT_077531->NM_147782

function

reference

NT_077531->NM_147783

function

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


reference	NT_077531->NM_001908->NP_001899	4197475	reverse	intron

reference	NT_077531->NM_147780->NP_680090	4197475	reverse	intron

reference	NT_077531->NM_147781->NP_680091	4197475	reverse	intron

reference	NT_077531->NM_147782->NP_680092	4197475	reverse	intron

reference	NT_077531->NM_147783->NP_680093	4197475	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1299525 maps exactly once on NCBI human chromosome 8

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
8	NW_001839122.2	335192	10653092	minus	A	alt_assembly_8	HuRef	HuRef	view	507
8	NW_923873.1	3638769	10851443	plus	C	alt_assembly_1	Celera	Celera	view	507
8	NT_077531.3	4197475	11759534	plus	C	ref_assembly	reference	reference	view	507

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077531 AF285442 AF285442.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AF285442.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss2073589	HapMap-CEU	European	120	IG	0.433	0.483	0.083	0.439	0.675		0.325

	HapMap-HCB	Asian	90	IG	0.267	0.467	0.267	0.655	0.500		0.500

	HapMap-JPT	Asian	88	IG	0.250	0.500	0.250	1.000	0.500		0.500

	HapMap-YRI	Sub-Saharan African	120	IG	0.250	0.383	0.367	0.100	0.442		0.558

	CHMJ	Asian	74	IG					0.554	0.041	0.405

ss23378697	AFD_EUR_PANEL	European	48	IG	0.333	0.583	0.083	0.251	0.625		0.375

	AFD_AFR_PANEL	African American	44	IG	0.182	0.591	0.227	0.403	0.477		0.523

	AFD_CHN_PANEL	Asian	48	IG	0.375	0.458	0.167	1.000	0.604		0.396

ss69039968	HapMap-CEU	European	120	GF	0.433	0.483	0.083		0.675		0.325

	HapMap-HCB	Asian	90	GF	0.267	0.467	0.267		0.500		0.500

	HapMap-JPT	Asian	90	GF	0.244	0.489	0.267		0.489		0.511

	HapMap-YRI	Sub-Saharan African	120	GF	0.250	0.383	0.367		0.442		0.558

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.497+/-0.038	332	260	270	0

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 .