Reference SNP(refSNP) Cluster Report: rs241174

Reference SNP(refSNP) Cluster Report: rs241174

refSNP ID: rs241174
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_018250.1:c.1564-563C>T
NT_023666.17:g.7003447G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44866479 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs241174 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
ss310544	KWOK\|OVLP-000621-371725	fwd/B	C/T	cttatttcatgaaacaggcctcacgtacca	ttgccaatctgcttaagtatcctaagctgc	06/30/00	10/10/03	79	Genomic	97 %
ss780956	SC_JCM\|AC040975.2_72325	fwd/B	C/T	cttatttcatgaaacaggcctcacgtacca	ttgccaatctgcttaagtatcctaagctgc	07/27/00	10/10/03	85	Genomic	unknown
ss1017506	KWOK\|OVLP-000804-256512	fwd/B	C/T	cttatttcatgaaacaggcctcacgtacca	ttgccaatctgcttaagtatcctaagctgc	09/02/00	10/10/03	86	Genomic	97 %
ss1962016	KWOK\|OVLP-000925-619488	fwd/B	C/T	cttatttcatgaaacaggcctcacgtacca	ttgccaatctgcttaagtatcctaagctgc	10/06/00	10/10/03	87	Genomic	97 %
ss17216465	CSHL-HAPMAP\|CSHL-HuAA-200402.chr8.NT_023666.16_7003447	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	02/17/04	03/04/04	120	Genomic	unknown
ss22733551	SSAHASNP\|WGSA-200403-chr8.chr8.NT_023666.16_7003447	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	03/21/04	03/21/04	121	Genomic	unknown
ss24092474	PERLEGEN\|afd1891807	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	08/10/04	09/13/04	123	Genomic	unknown
ss44866479	ABI\|hCV2611026	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	07/19/05	11/03/06	126	Genomic	unknown
ss66082609	AFFY\|SNP_A-1919438	rev/T	A/G	ttaagcagattggcaa	tggtacgtgaggcctg	10/27/06	08/14/07	127	Genomic	unknown
ss69045697	PERLEGEN\|PGP01891807	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	01/30/07	08/14/07	127	Genomic	unknown
ss76025751	AFFY\|AFFY_6_1M_SNP_A-1919438	rev/T	A/G	ttaagcagattggcaa	tggtacgtgaggcctg	08/28/07	08/29/07	129	Genomic	unknown
ss80369323	HGSV\|Cor18507_SNV_20070510.chr8_28685079	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	11/23/07	11/25/07	130	Genomic	unknown
ss84602574	HGSV\|Cor19240_SNV_20070510.chr8_28685079	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	11/30/07	12/07/07	130	Genomic	unknown
ss93862617	BCMHGSC_JDW\|JWB-2447207	rev/T	A/G	gcagcttaggatacttaagcagattggcaa	tggtacgtgaggcctgtttcatgaaataag	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGTTGCAATG AGCTATGATC ACACCACCAC ACTCCAGCCT GGGCAGCAGA GTGAGGCCCC
 ATCTCAAAAA AAAAAAGACT CCTTCAGAGT CGTCTTGGAA ATAGTGCATG GCTGCCCAGG
 GAGAGCGCAG AACGCCATCC CCAAAGCTCC CACCCCAGCC TTGTGCAGGG AGGAGGGGCC
 TGTGTGGAGG AGGCCTCAGG TGAAGAACGG GATCTGGCGC ACACCCTGCT CCTCGGCAAG
 GGCCGCTTCA CGCTCGCCAT AGGCCGTTTT CTTATTTCAT GAAACAGGCC TCACGTACCA
 Y
 TTGCCAATCT GCTTAAGTAT CCTAAGCTGC TTCCTCTGCC CGTTTGGTAT TGATCTTCAT
 GTTTACATAA TGGCCTCTTG CATGTTTTTG TTTTTAAATA AAGGTGGCTT GGCTAGGTAG
 GGGTCTACAT GTCTTAAAAA CCATGCAGCT AAACCCAGCA ACAGAGCACC TAATAAGGTC
 AGGCTGCACG GCAGGGCACC CATCAGGTGC AGGTGGTCGG AAAGATACCA CCCCCCAGGT
 AAAGCCGTGG CTCCCACCAT CAGGAGAAGT CAGACTTTCA GGAAGAGAGA GCTCCCTCAA

GeneView

GeneView via analysis of contig annotation: INTS9 integrator complex subunit 9

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_023666->NM_018250

function

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


reference	NT_023666->NM_018250->NP_060720	7003447	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs241174 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_001839127.1	7007799	27174698	minus	A	alt_assembly_8	HuRef	HuRef	view	300
8	NW_923907.1	16156848	27589010	minus	A	alt_assembly_1	Celera	Celera	view	300
8	NT_023666.17	7003447	28685079	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023666 U96629 U96629.1

dbSNP Blast Analysis
GenBank HTGS Finished:
U96629.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24092474	AFD_EUR_PANEL	European	48	IG	0.292	0.500	0.208	1.000	0.542	0.458

	AFD_AFR_PANEL	African American	46	IG	0.435	0.435	0.130	1.000	0.652	0.348

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.375	0.292	0.251	0.521	0.479

ss44866479	HapMap-CEU	European	120	IG	0.300	0.517	0.183	0.752	0.558	0.442

	HapMap-HCB	Asian	86	IG	0.302	0.512	0.186	1.000	0.558	0.442

	HapMap-JPT	Asian	90	IG	0.156	0.533	0.311		0.422	0.578

	HapMap-YRI	Sub-Saharan African	118	IG	0.407	0.525	0.068	0.200	0.669	0.331

ss66082609	HapMap-CEU	European	118	GF	0.305	0.525	0.169		0.568	0.432

	HapMap-HCB	Asian	90	GF	0.289	0.511	0.200		0.544	0.456

	HapMap-JPT	Asian	90	GF	0.156	0.533	0.311		0.422	0.578

	HapMap-YRI	Sub-Saharan African	120	GF	0.417	0.517	0.067		0.675	0.325

ss69045697	HapMap-CEU	European	120	GF	0.300	0.517	0.183		0.558	0.442

	HapMap-HCB	Asian	90	GF	0.289	0.511	0.200		0.544	0.456

	HapMap-JPT	Asian	90	GF	0.156	0.533	0.311		0.422	0.578

	HapMap-YRI	Sub-Saharan African	120	GF	0.417	0.517	0.067		0.675	0.325

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.492+/-0.061	332	260	270	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .