Reference SNP(refSNP) Cluster Report: rs1019264

Reference SNP(refSNP) Cluster Report: rs1019264

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:	C
Clinical Association:	unknown

HGVS Names
NT_022184.14:g.38828735G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5157426 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1019264 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
ss1483373	TSC-CSHL\|TSC0222995	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	09/07/00	10/25/06	86	Genomic	95 %
ss5157426	TSC-CSHL\|TSC0249571	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	09/19/02	10/25/06	108	Genomic	unknown
ss5730154	SC_JCM\|NT_005375.10_2604899	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	01/10/03	10/10/03	111	Genomic	unknown
ss19448173	CSHL-HAPMAP\|CSHL-HuDD-200402.chr2.NT_022184.13_38828734	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	02/20/04	03/04/04	120	Genomic	unknown
ss24637787	PERLEGEN\|afd0729706	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	08/10/04	09/13/04	123	Genomic	unknown
ss44207172	ABI\|hCV2202431	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	07/18/05	11/03/06	126	Genomic	unknown
ss66875225	ILLUMINA\|HumanHap550v1.1_rs1019264	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	11/14/06	11/14/06	127	Genomic	unknown
ss66957897	ILLUMINA\|HumanHap650Yv1.0_rs1019264	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	11/14/06	11/14/06	127	Genomic	unknown
ss68080818	ILLUMINA\|HumanHap250Sv1.0_rs1019264	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	12/06/06	12/07/06	127	Genomic	unknown
ss68816283	PERLEGEN\|PGP00729706	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	01/30/07	08/14/07	127	Genomic	unknown
ss70470798	ILLUMINA\|HumanHap550v3.0__rs1019264	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	04/20/07	03/29/08	130	Genomic	unknown
ss70992507	ILLUMINA\|HumanHap650Yv3.0_rs1019264	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	04/23/07	04/23/07	127	Genomic	unknown
ss74912192	ILLUMINA\|ILMN_Human_1M_rs1019264	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	08/28/07	08/29/07	129	Genomic	unknown
ss81962802	HGSV\|Cor18555_SNV_20070510.chr2_59924453	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	11/27/07	12/01/07	130	Genomic	unknown
ss83660953	KRIBB_YJKIM\|KHS513124	fwd/B	C/T	agatctgaaagtagaaccaatcaaggctcc	actgtgggccagagcatcttgagctgggta	12/04/07	12/05/07	130	Genomic	unknown
ss91181016	BCMHGSC_JDW\|JWB-1249057	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	02/26/08	03/01/08	129	Genomic	unknown
ss109563391	1000GENOMES\|CEU.trio.12.15.2008_390720_chr2_59866306	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	12/15/08	12/16/08	130	Genomic	unknown
ss117728519	ILLUMINA-UK\|NA18507_000088888_NCBI36.1_chr2_59866306	rev/T	A/G	tacccagctcaagatgctctggcccacagt	ggagccttgattggttctactttcagatct	01/19/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 CTTAGAAAGC ATGCCTTGAT CAAAGTGTTT ATTGATACTA GCACATGCAG AAGAATCTTT
 GTGGAAGAAA CAGTACTATC TCTTCTTTAA AGATCTGAAA GTAGAACCAA TCAAGGCTCC
 Y
 ACTGTGGGCC AGAGCATCTT GAGCTGGGTA GAACAATATT CCCAGGCTAC ATTTTCAGGG
 ACCCTCCTGC AAATAAAGGG GGATTTCCTT TTCCCTTCTA CAGCCTGCTT CTTAAAACCA
 AGTGGAATCT GCCACATAAT TGTTTCCATA AGGAGAGGCT TCATTCTGTG TCTGAATCCT
 TTATGCCCTC ATGTCCCTGA GCACGCCTTT CCAAACAGCA GTATGCGGAA AGTCAGTGGA
 ATGGGCGCCA CAGTCTGGGA CCCCCTACAG TGGATAGAAA AAAACGAGGT CCCAATGCTA
 GTGCTTGGAT CAAAAGAGAA GCAAACAGAA TGGTTACACT CAGAAGACCT CTATAGGTCT
 GGTTATTTAT TACCATCATC AAGCAATATT GATATATTTA TTCTTTAATA AAAGCTGACC
 ACCCACAGAA TCTGAGGGAG AAATCTTGAC ATTTAGCTCA GGTTTTCAGG GTGAAATTGT
 TGCTGTTATA GTAAATAGAA TTACTTAATG TTGACTTTCT TCCTGGGGGG TAGCATGTAT
 GTGTTAGTGT CCTCTATACC CATGTTTAAA GCCTAAGTac acacacatgc ctacacatat
 acacatacac acacatacat atacaGAAAA AATATGTATG CCTAAAAGTG TGTATACAAC
 TTAAAATATG AAAAATTTCC AGGCCTTCCA CCATGGCCCA CAGCATGTTT AGATTTCTAG
 TGTCTTTTAT GTCTGTAGTG TGGTATTTTT TCTCAAAACA TTAACTTTTC ACATTCTGAA
 AGTTGTATGT GTTGATTACG GAACATTTGG AAAGTGTAAG AAAATACAAA GGGAAAAATA
 AAAATCACAC AAAAATCACA TAATACCATC ATGCAAAGAG AACCACTACT CATGTTTTGG
 TGCTATTGTT TTTATGTAGC TTACTTTTAA ATTTTGGTTG TCTCCAACCT GTTATTCTCT
 TTGAGGAAAG TGGCATACCT TTAGGTGAAA CAAATGGTGG CATAATTAGT CTATTCGTTT
 TGCTATTTTA AGACAGTGCA CATTATCTTT AACAGTCTTC TCTGAAGTAC ATGACCATTT
 TCCATCTCTC ATCCATTCAT CATTCACCAT TCATCAT

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_022184 AC015740.3

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
ss1483373	TSC_42_AA		82	AF					0.512	0.488

	TSC_42_C		78	AF					0.551	0.449

	TSC_42_A		72	AF					0.389	0.611

ss24637787	AFD_EUR_PANEL	European	48	IG	0.333	0.417	0.250	0.439	0.542	0.458

	AFD_AFR_PANEL	African American	46	IG	0.261	0.565	0.174	0.527	0.543	0.457

	AFD_CHN_PANEL	Asian	48	IG	0.417	0.375	0.208	0.294	0.604	0.396

ss44207172	AoD_African_American		90	AF					0.540	0.460

	AoD_Caucasian		92	AF					0.590	0.410

	AoD_Chinese		90	AF					0.510	0.490

	AoD_Japanese		90	AF					0.670	0.330

ss5157426	HapMap-CEU	European	120	IG	0.367	0.417	0.217	0.254	0.575	0.425

	HapMap-HCB	Asian	90	IG	0.356	0.489	0.156	1.000	0.600	0.400

	HapMap-JPT	Asian	90	IG	0.289	0.556	0.156	0.403	0.567	0.433

	HapMap-YRI	Sub-Saharan African	120	IG	0.367	0.483	0.150	1.000	0.608	0.392

	CHMJ	Asian	74	IG					0.527	0.473

ss68816283	HapMap-CEU	European	120	GF	0.367	0.417	0.217		0.575	0.425

	HapMap-HCB	Asian	90	GF	0.356	0.489	0.156		0.600	0.400

	HapMap-JPT	Asian	90	GF	0.289	0.556	0.156		0.567	0.433

	HapMap-YRI	Sub-Saharan African	120	GF	0.367	0.483	0.150		0.608	0.392