Reference SNP(refSNP) Cluster Report: rs1075665

Reference SNP(refSNP) Cluster Report: rs1075665

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_012381.2:c.1517-22A>G
NM_181837.1:c.1517-19C>A
NT_007299.12:g.26186773A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52067891 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1075665 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
ss78065	TSC-CSHL\|TSC0021586	fwd/B	C/T	ctttggtttctgcttttaatacaaaaccag	agacatcaatgagggtaaatccaagtcaag	09/06/00	10/25/06	86	Genomic	95 %
ss3255235	UWGC\|orc3l-e15-f22	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	09/06/01	04/07/04	100	Genomic	unknown
ss6183260	SC_JCM\|NT_007299.10_5017829	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	01/10/03	10/10/03	111	Genomic	unknown
ss13066218	SC_SNP\|NT_007299.12_26186773	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	10/22/03	10/31/03	119	Genomic	unknown
ss22459417	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007299.12_26186773	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	03/21/04	03/21/04	121	Genomic	unknown
ss35034425	EGP_SNPS\|ORC3L-068767	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	02/09/05	11/02/06	125	Genomic	unknown
ss44704567	ABI\|hCV11568848	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	07/19/05	11/03/06	126	Genomic	unknown
ss52067891	SI_EXO\|NT_007299.12_26186773	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	03/29/06	08/14/07	127	Genomic	unknown
ss65748229	ILLUMINA\|Human1-rs1075665	fwd/B	C/T	ctttggtttctgcttttaatacaaaaccag	agacatcaatgagggtaaatccaagtcaag	10/10/06	10/10/06	127	Genomic	unknown
ss66858771	EGP_SNPS\|ORC3L_068767	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	11/09/06	12/16/06	127	Genomic	unknown
ss75017096	ILLUMINA\|ILMN_Human_1M_rs1075665	fwd/B	C/T	ctttggtttctgcttttaatacaaaaccag	agacatcaatgagggtaaatccaagtcaag	08/28/07	08/29/07	129	Genomic	unknown
ss80757682	KRIBB_YJKIM\|KHS1002944	fwd/B	C/T	ctttggtttctgcttttaatacaaaaccag	agacatcaatgagggtaaatccaagtcaag	11/26/07	11/26/07	130	Genomic	unknown
ss98518029	HUMANGENOME_JCVI\|1103652928931	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	04/01/08	04/01/08	130	Genomic	unknown
ss114709695	1000GENOMES\|NA19240_2008_12_16_1406424_chr6_88423321	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	12/18/08	12/18/08	130	Genomic	unknown
ss116594234	ILLUMINA-UK\|NA18507_000124102_NCBI36.1_chr6_88423321	rev/T	A/G	cttgacttggatttaccctcattgatgtct	ctggttttgtattaaaagcagaaaccaaag	01/17/09	01/17/09	130	Genomic	99 %

Fasta sequence (Legend)

 CAGATTTGTG CAGCCATGTT CCCATTTTCT CTTATTGCTA GCTGATTCTC TTTCTCTTGC
 TGAGCCCACA GGAATGGTTT CCACCTATGT TAGCTAGTAG GTTCCAGAAT GTGTATATGT
 AGAGTAATGA TGGCAATGGG ACTAACAGGA TGTTCAACTT AGAAGTGAGT TAAAAGTCTG
 CTTTGTTCCT GGTTGTGGTT TAAAAATGAA AACAAAAACA TCCAGGCAGA GTTAATCTAG
 AGCACAAACT GAAAAAAGGG AGTGTCACAG GATGCAGCTG GAAGGGAAGA GAGTGACCTG
 ACCTTCTGAA GATGATAGAG GTCTGTCTTC TGAAGCCCCT TTGGCTGTGA CCCAGAAGCA
 TCTTCTTCCT CTTTGGTTTC TGCTTTTAAT ACAAAACCAG
 Y
 AGACATCAAT GAGGGTAAAT CCAAGTCAAG GGAACAAACA TTTCTACTAC TCCAAAGTAA
 AAGTTTCACC TATATATATT TTTTTAATGT GGCAAGGGAT CAAGATTCCA TCTGATAAAT
 GATTTCTTAC AGAAGCTGAA GGCCAATAAT ATATAACTTG TGCTGTAGTG ATGTCTTCAA
 AAAATCAGCT ACTGAATTTT AAAAGTGTAA CCACAATGAA AACAAAACAA AATACAACCT
 AACAAAACTC CCTCAAACCA ACAGCAAAAA GTCTCAAAAA AAAAAATTTT TTTTTTTCAG
 ATGGAGTCTT GCTCTGTTGC CCAGGCTGGA GTGCAGTGGC GCCATCTTGG CTCACTGCAA
 CCTCCTCCTC CCAGTTCAAG TGCTTCTCCT GCCTCAGCCT

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_007299.12 ABBA01040503 AL356970.2

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
ss3255235	NIHPDR	Global	172	IG	0.151	0.500	0.349	0.752	0.401	0.599

ss35034425	PDR90	Global	178	IG	0.146	0.494	0.360	0.752	0.393	0.607

ss44704567	AoD_African_American		90	AF					0.340	0.660

	AoD_Caucasian		92	AF					0.320	0.680

	AoD_Chinese		90	AF					0.310	0.690

	AoD_Japanese		90	AF					0.330	0.670

ss52067891	HapMap-CEU	European	120	IG	0.083	0.350	0.567		0.258	0.742

	HapMap-HCB	Asian	88	IG	0.068	0.523	0.409		0.330	0.670

	HapMap-JPT	Asian	90	IG	0.111	0.489	0.400		0.356	0.644

	HapMap-YRI	Sub-Saharan African	118	IG	0.102	0.475	0.424		0.339	0.661

ss66858771	HSP_GENO_PANEL		120	IG	0.150	0.417	0.433	0.479	0.358	0.642

	CEU_GENO_PANEL	European	120	IG	0.083	0.350	0.567	0.527	0.258	0.742

	AAM_GENO_PANEL	African American	124	IG	0.097	0.355	0.548	0.403	0.274	0.726

	CHB_GENO_PANEL	Asian	90	IG	0.089	0.511	0.400	0.403	0.344	0.656

	YRI_GENO_PANEL	Sub-Saharan African	120	IG	0.100	0.483	0.417	0.584	0.342	0.658

	JPT_GENO_PANEL	Asian	90	IG	0.111	0.489	0.400	0.655	0.356	0.644

ss78065	TSC_42_AA		82	AF					0.366	0.634

	TSC_42_C		84	AF					0.321	0.679

	TSC_42_A		80	AF					0.288	0.712

ss80757682	KHP1		180	AF					0.322	0.678