Reference SNP(refSNP) Cluster Report: rs702490

Reference SNP(refSNP) Cluster Report: rs702490

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_147193.1:c.-267+4559G>T
NT_032977.8:g.24166937A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43941229 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs702490 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
ss1047770	KWOK\|OVLP-000804-49916	rev/T	A/G	tgccccaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	09/02/00	10/10/03	86	Genomic	96 %
ss1364491	TSC-CSHL\|TSC0243017	fwd/B	C/T	tttgtacttacggagcgctctttgtgagaa	atctctgtgctagggcttctcgttgaggca	09/06/00	04/07/04	86	Genomic	95 %
ss1642888	KWOK\|OVLP-000925-463976	fwd/B	C/T	tttgtacttacggagcgctctttgtgagaa	atctctgtgctagggcttctcgttgaggca	10/04/00	10/10/03	87	Genomic	97 %
ss1642937	KWOK\|OVLP-000925-464566	rev/T	A/G	tgccccaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	10/04/00	10/10/03	87	Genomic	97 %
ss2643423	SC_JCM\|AL391003.5_67674	rev/T	A/G	tgccccaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	11/03/00	10/10/03	89	Genomic	unknown
ss13040155	SC_SNP\|NT_032977.5_6643930	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	10/22/03	10/31/03	119	Genomic	unknown
ss15396425	SC_SNP\|NT_032977.6_15758089	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	11/14/03	11/22/03	120	Genomic	unknown
ss16402403	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_032977.6_15758089	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	02/17/04	03/04/04	120	Genomic	unknown
ss20600925	SSAHASNP\|WGSA-200403-chr1.chr1.NT_032977.6_15758089	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	03/18/04	03/18/04	121	Genomic	unknown
ss43941229	ABI\|hCV2525074	rev/T	A/G	tgccccaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	07/18/05	11/03/06	126	Genomic	unknown
ss68766010	PERLEGEN\|PGP00678598	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	01/30/07	08/14/07	127	Genomic	unknown
ss75159287	ILLUMINA\|ILMN_Human_1M_rs702490	fwd/B	C/T	tttgtacttacggagcgctctttgtgagaa	atctctgtgctagggcttctcgttggggca	08/28/07	08/29/07	129	Genomic	unknown
ss77609250	HGSV\|Cor12156_SNV_20070510.chr1_53907039	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	10/09/07	10/13/07	129	Genomic	unknown
ss83765517	HGSV\|Cor18956_SNV_20070510.chr1_53907039	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	11/30/07	12/05/07	130	Genomic	unknown
ss87430039	BCMHGSC_JDW\|JWB-0045890	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	02/26/08	02/26/08	129	Genomic	unknown
ss97936809	HUMANGENOME_JCVI\|1103675094828	rev/T	A/G	tgccccaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	03/30/08	03/30/08	130	Genomic	unknown
ss106566302	BGI\|BGI_rs702490	rev/T	A/G	tgccccaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	09/16/08	06/16/09	130	Genomic	unknown
ss108196583	1000GENOMES\|CEU.trio.12.15.2008_63947_chr1_53967606	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	12/15/08	12/15/08	130	Genomic	unknown
ss110443617	1000GENOMES\|NA19240_2008_12_16_61846_chr1_53967606	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	12/16/08	12/17/08	130	Genomic	unknown
ss118690555	ILLUMINA-UK\|NA18507_000059098_NCBI36.1_chr1_53967606	rev/T	A/G	tgcctcaacgagaagccctagcacagagat	ttctcacaaagagcgctccgtaagtacaaa	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 ATTCAAGGCA TCGTCTTCTG ATTTATTTTT TAAAGGGAAA AGGTCATAAA ATAAGTTGCT
 TTATGTGCTG ATGGATTAAG TGGCTTAGGC TGAAATAACA GCAGGAACTT TACTATTTTT
 CCCTGTTTTA ACAATGCTTT TTGGGGGAGG GGGGTGGGTC TTTTTCCCGC CTGCTTGTCT
 CCTCCCTCCG TACCCCCCGT CAACCCCAGC CAGATGGCTT TAATTCTAAC CAAATCCCAC
 GCTGAGGCCA AATGATTGAT CAAACAGTCA TTTGTACTTA CGGAGCGCTC TTTGTGAGAA
 Y
 ATCTCTGTGC TAGGGCTTCT CGTTGGGGCA GGCTCTTCTT TGGGCCTTCA AACGGATGAT
 TTCAAACAGA TCGAGCGGCT TGGTGAGGAG GGGTCCGCGG GTGGATGCGG AGCAAAAATC
 CCAGACCTCA AGTCCGTAGA ACTTCTCGCT TAAAACCTCT GTGTTACTTC CCATCCCTGA
 CAGCAGGGGT ATCCAAATGT TCTAAGTATA AGGACAAAAA TCTTTCCACT GTCCACGTGA
 CAGCATCTAT ACTTTTAGTA TCTCTTGAAG CAGAATATAC CTAATGAGGT TTAGGTAACT

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_032977 ABBA01074736 AC073554 AL049745 AL049745.9 AL391003.5

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
ss1364491	TSC_42_AA		81	AF					0.673	0.327

	TSC_42_C		82	AF					0.585	0.415

	TSC_42_A		78	AF					0.470	0.530

ss43941229	HapMap-CEU	European	100	IG	0.580	0.320	0.100	0.317	0.740	0.260

	HapMap-HCB	Asian	78	IG	0.282	0.513	0.205	1.000	0.538	0.462

	HapMap-JPT	Asian	86	IG	0.349	0.535	0.116	0.403	0.616	0.384

	HapMap-YRI	Sub-Saharan African	112	IG	0.375	0.482	0.143	1.000	0.616	0.384

ss68766010	HapMap-CEU	European	120	GF	0.500	0.350	0.150		0.675	0.325

	HapMap-HCB	Asian	90	GF	0.289	0.533	0.178		0.556	0.444

	HapMap-JPT	Asian	90	GF	0.333	0.556	0.111		0.611	0.389

	HapMap-YRI	Sub-Saharan African	120	GF	0.383	0.483	0.133		0.625	0.375