Reference SNP(refSNP) Cluster Report: rs1079861

Reference SNP(refSNP) Cluster Report: rs1079861

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
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_052917.2:c.143-63061C>A
NT_005403.16:g.5143207A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss21685557 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1079861 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
ss150257	TSC-CSHL\|TSC0066071	fwd/B	C/T	cccaggcaattaatgagtctggtaaaccta	aaaaacttgcaaatcaaaactcccctaaaa	09/06/00	04/07/04	86	Genomic	95 %
ss5536435	TSC-CSHL\|TSC0494251	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	09/21/02	10/10/03	110	Genomic	unknown
ss6201327	SC_JCM\|NT_005151.10_1874992	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	01/10/03	10/10/03	111	Genomic	unknown
ss21685557	SSAHASNP\|WGSA-200403-chr2.chr2.NT_005403.14_5143207	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	03/20/04	10/26/06	121	Genomic	unknown
ss24310092	PERLEGEN\|afd0769706	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	08/10/04	09/13/04	123	Genomic	unknown
ss44268887	ABI\|hCV3197591	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	07/18/05	07/18/05	126	Genomic	unknown
ss65947182	AFFY\|SNP_A-1730921	fwd/B	C/T	gcaattaatgagtctggtaaaccta	aaaaacttgcaaatcaaaactcccc	10/26/06	10/26/06	127	Genomic	unknown
ss68832046	PERLEGEN\|PGP00769706	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	01/30/07	08/14/07	127	Genomic	unknown
ss77712150	HGSV\|Cor12156_SNV_20070510.chr2_154759297	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	10/09/07	10/14/07	129	Genomic	unknown
ss80463294	HGSV\|Cor18507_SNV_20070510.chr2_154759297	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	11/23/07	11/25/07	130	Genomic	unknown
ss97090397	HUMANGENOME_JCVI\|1103658259490	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	03/28/08	03/28/08	130	Genomic	unknown
ss106130058	BGI\|BGI_rs1079861	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	09/13/08	06/18/09	130	Genomic	unknown
ss110089205	1000GENOMES\|CEU.trio.12.15.2008_500832_chr2_154642035	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	12/15/08	12/17/08	130	Genomic	unknown
ss111127383	1000GENOMES\|NA19240_2008_12_16_453628_chr2_154642035	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	12/16/08	12/17/08	130	Genomic	unknown
ss117931703	ILLUMINA-UK\|NA18507_000192328_NCBI36.1_chr2_154642035	rev/T	A/G	ttttaggggagttttgatttgcaagttttt	taggtttaccagactcattaattgcctggg	01/19/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 CACTAAAAAT AATTCTAGAA GATAAATATG TCATTAAAAT CTGTGGGTAT TTCCAAAGCA
 TACATTCCTT GATGTCAATG ACTAAGAACA TGTATAAATT CTTGTGTGTT TTTCATTTTa
 aactacttgc cacaaaattt gtgtctattt aaattctcac cagccatata agagaatgct
 catttgacca atcccttaca accattcaat attatatttt aaaatctttg ccaattcaat
 agatgaaaat gacatcttat tttattttcc acccctttac tcacaaataa gggcacaaat
 gatatggaat aattttttgt gtctttatta ttatcttgca tgtctcttgg gaattacctg
 attctattca gacctcatga tcacttctcc atgaggaatt tatatttcac ttttaagttt
 tCCAATTTCA AAGATTAGAC ATAAACCAAA GGAAATCCTG TAAAGTTCTT CCCAGGCAAT
 TAATGAGTCT GGTAAACCTA
 Y
 AAAAACTTGC AAATCAAAAC TCCCCTAAAA GTTCCTAATA TATAAACAAG CAATGTTAAA
 ATTAGAGATT TTATAGTTTG TATACTCAGC CGCATTTATA CATTCCTCCA CTAAGCACAC
 AAAACAATAA GCATATAAGC TCAAGTCTAG AAGTTTTGCT TCTTTTCACT GTTATACTAA
 TAAATTCCTA GTGTGTTTTG

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_005403 ABBA01004809 AC009421.2 AC068437.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss150257	TSC_42_AA		82	AF					0.476	0.524

	TSC_42_C		82	AF					0.317	0.683

	TSC_42_A		82	AF					0.707	0.293

	AfAm	African American	38	IG	0.263	0.316	0.421	0.150	0.421	0.579

	Caucasian	European	40	IG	0.150	0.200	0.650	0.050	0.250	0.750

	Asian	Asian	40	IG	0.500	0.350	0.150	0.371	0.675	0.325

	CEPH	European	54	IG	0.074	0.481	0.444	0.584	0.315	0.685

	PDpanel	Global	48	IG	0.292	0.417	0.292	0.439	0.500	0.500

ss21685557	HapMap-CEU	European	120	IG	0.150	0.350	0.500	0.150	0.325	0.675

	HapMap-HCB	Asian	90	IG	0.556	0.400	0.044	0.584	0.756	0.244

	HapMap-JPT	Asian	88	IG	0.568	0.364	0.068	1.000	0.750	0.250

	HapMap-YRI	Sub-Saharan African	120	IG	0.350	0.400	0.250	0.150	0.550	0.450

ss24310092	AFD_EUR_PANEL	European	46	IG	0.087	0.609	0.304	0.200	0.391	0.609

	AFD_AFR_PANEL	African American	42	IG	0.333	0.571	0.095	0.343	0.619	0.381

	AFD_CHN_PANEL	Asian	48	IG	0.417	0.583		0.050	0.708	0.292

ss68832046	HapMap-CEU	European	120	GF	0.150	0.350	0.500		0.325	0.675

	HapMap-HCB	Asian	90	GF	0.556	0.400	0.044		0.756	0.244

	HapMap-JPT	Asian	90	GF	0.556	0.356	0.089		0.733	0.267

	HapMap-YRI	Sub-Saharan African	120	GF	0.350	0.400	0.250		0.550	0.450