Reference SNP(refSNP) Cluster Report: rs1941973

Reference SNP(refSNP) Cluster Report: rs1941973

refSNP ID: rs1941973
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	92/129
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
NM_020774.2:c.2587-671C>T
NT_010966.13:g.921532C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44066968 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1941973 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
ss2833544	TSC-CSHL\|TSC1012789	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	01/03/01	04/07/04	92	Genomic	unknown
ss10889087	BCM_SSAHASNP\|chr18.NT_010966.13_921532	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	06/30/03	10/10/03	116	Genomic	unknown
ss14829695	SC_SNP\|NT_010966.13_921532	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	11/12/03	11/22/03	119	Genomic	unknown
ss17604252	CSHL-HAPMAP\|CSHL-HuCC-200402.chr18.NT_010966.13_921532	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	02/19/04	03/04/04	120	Genomic	unknown
ss21451110	SSAHASNP\|WGSA-200403-chr18.chr18.NT_010966.13_921532	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	03/20/04	03/20/04	121	Genomic	unknown
ss23468626	PERLEGEN\|afd4172349	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	08/10/04	09/13/04	123	Genomic	unknown
ss44066968	ABI\|hCV2020244	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	07/18/05	11/03/06	126	Genomic	unknown
ss65785978	ILLUMINA\|Human1-rs1941973	fwd/T	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	10/10/06	10/10/06	127	Genomic	unknown
ss68427280	CSHL-HAPMAP\|illumina:assay:44546:1	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	01/11/07	01/16/07	127	NA	unknown
ss74987372	ILLUMINA\|ILMN_Human_1M_rs1941973	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	08/28/07	08/29/07	129	Genomic	unknown
ss90729144	BCMHGSC_JDW\|JWB-1075181	fwd/B	C/T	tgagtagccaagggctatggggtagggata	aggaagccagagccaaggtggttaatagtt	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGAGGTAGAT TTTGAATCCA GGAATGTCAG TGTCTTGATC AACTATGTCT TACTGCATTC
 TGCATTCTGC TTTTTCTATA CTTACATAAA TTCTATGTAC ATACTGAGGT GTAAGTTGGG
 AAAGTCCATA GAGAGAAAGA GAGAGAGCAC ACGTGCATGT ATTTGGTTGT TTGGATGATG
 CTGTAGGTGA GTAGTAGTTA CCATTTTTGG TGACACAAGA GATGGCTAAA TGTGACTGTG
 TGTTAGAAGG GAGAATAGGT GAAAGACAGA TGAGTAGCCA AGGGCTATGG GGTAGGGATA
 Y
 AGGAAGCCAG AGCCAAGGTG GTTAATAGTT AAATGTCCAA GCTCAGATTA AGTGGACATG
 AAGAAGAGGT GAAAGTGAGG GAGATTATGA ATAGGCTGTG GAAGTCTTGC TAGAGATCAG
 GGAAAAAGAA TAGCCCAAAG CTGTGGGCTT CAGGCAGCAT GGGAATTGAC CAAGTCCTGG
 AAAAGGGCAC TTTAAGGTAG AGTTTCTTAA ATGTGGGTAA ACAGAAAAAT CCCTCTTGGA
 TTTTAGCAAT TTGGCTAATC TAGCTAGATT TTTATTAATA TTAGAAATCT GTCTTTCAGT

GeneView

GeneView via analysis of contig annotation: MIB1 mindbomb homolog 1 (Drosophila)

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_010966->NM_020774

function

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


reference	NT_010966->NM_020774->NP_065825	921532	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1941973 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_927095.1	906883	16238478	plus	T	alt_assembly_1	Celera	Celera	view	300
18	NW_001838467.2	25120994	16279808	minus	A	alt_assembly_8	HuRef	HuRef	view	300
18	NT_010966.13	921532	17686428	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010966

dbSNP Blast Analysis
GenBank HTGS Draft:
AP001352.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23468626	AFD_EUR_PANEL	European	48	IG		0.250	0.750	0.527	0.125	0.875

	AFD_AFR_PANEL	African American	44	IG	0.091	0.318	0.591	0.479	0.250	0.750

	AFD_CHN_PANEL	Asian	48	IG		0.250	0.750	0.527	0.125	0.875

ss2833544	CEPH		93	AF					0.139	0.861

ss44066968	HapMap-CEU	European	116	IG		0.172	0.828	0.527	0.086	0.914

	HapMap-HCB	Asian	90	IG	0.022	0.111	0.867	0.150	0.078	0.922

	HapMap-JPT	Asian	88	IG		0.227	0.773	0.403	0.114	0.886

	HapMap-YRI	Sub-Saharan African	118	IG	0.169	0.458	0.373	0.752	0.398	0.602

	AoD_Chinese		90	AF					0.090	0.910

	AoD_Japanese		90	AF					0.070	0.930

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.290+/-0.247	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .