Reference SNP(refSNP) Cluster Report: rs6786582

Reference SNP(refSNP) Cluster Report: rs6786582

refSNP ID: rs6786582
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
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_018133.2:c.142+14830A>G
NT_005612.15:g.42394130T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10056691 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6786582 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
ss10056691	BCM_SSAHASNP\|chr3.NT_005612.13_42298520	fwd/B	C/T	actcatgaatgttaaaaatgtaggctaaaa	ggcatacattacacaggggcaaaactgcct	06/27/03	04/07/04	116	Genomic	unknown
ss14196449	BCM_SSAHASNP\|chr3.NT_005612.14_42394138	fwd/B	C/T	actcatgaatgttaaaaatgtaggctaaaa	ggcatacattacacaggggcaaaactgcct	11/05/03	11/22/03	119	Genomic	unknown
ss24317471	PERLEGEN\|afd3120831	fwd/B	C/T	actcatgaatgttaaaaatgtaggctaaaa	ggcatacattacacaggggcaaaactgcct	08/10/04	09/13/04	123	Genomic	unknown
ss66116249	AFFY\|SNP_A-2025907	fwd/B	C/T	aaaatgtaggctaaaa	ggcatacattacacag	10/27/06	03/31/08	127	Genomic	unknown
ss68876385	PERLEGEN\|PGP03120831	fwd/B	C/T	actcatgaatgttaaaaatgtaggctaaaa	ggcatacattacacaggggcaaaactgcct	01/30/07	03/31/08	127	Genomic	unknown
ss75157634	ILLUMINA\|ILMN_Human_1M_rs6786582	fwd/B	C/T	actcatgaatgttaaaaatgtaggctaaaa	ggcatacattacacaggggcaaaactgcct	08/28/07	08/29/07	129	Genomic	unknown
ss76103229	AFFY\|AFFY_6_1M_SNP_A-2025907	fwd/B	C/T	aaaatgtaggctaaaa	ggcatacattacacag	08/28/07	08/30/07	130	Genomic	unknown

Fasta sequence (Legend)

 AATGATTTGA AGGAAAAAAA ACTACTTTTA ATCAGCATAT TAGGCAAGAT TATACTATAA
 AGATCATCTT AAAGCATACA AAGACAATTT TATCTAAATT AAGTTTTAAA ATGCATTTGT
 TGACATATCT ACTTTAAAAC GGCTTATCTT Gggctgggca tggtgctcac acctgtaatc
 acagcacttt gggaggccaa ggcaggtgat cacctgaggt caagagtttg agatcagcct
 ggccaacacg gtgaaactcc acctctacta aaaatacaaa aactagccag gcgtggtggc
 gggggcctgt agtcccagct actcaagagg ctgaggcaag agaacacttg aacccaggag
 gcagaggttg cagtgagctg agatccctcc actgcactcc agcttgggca acagagcgag
 actccgtctc aaaaaaaaaa taaaaaataa aaataaaaTG GCATGCCCTG TTTGTAAACT
 CATGAATGTT AAAAATGTAG GCTAAAA
 Y
 GGCATACATT ACACAGGGGC AAAACTGCCT ATGTACCCTG ATATTTGGAC TTCTTATGTT
 TCCGACTAAA ATTTTTTTTT AACAATTTTT GTATTTTGTT ACTACGTGAT AAGCTAAAAG
 TGGCTTCAAA ACGGCATCTA CAAACACTTC AAATAACACA TTCCAAGTAT GAACAGTCTC
 TGGTCTCCAA AAATAAAAAG

GeneView

GeneView via analysis of contig annotation: MSL2L1 male-specific lethal 2-like 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_005612->NM_018133

function

HuRef

NW_001838884->NM_018133

function

Celera

NW_921807->NM_018133

function

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


reference	NT_005612->NM_018133->NP_060603	42394130	reverse	intron

HuRef	NW_001838884->NM_018133->NP_060603	58152702	forward	intron

Celera	NW_921807->NM_018133->NP_060603	42509826	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6786582 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_001838884.2	58152702	133276329	minus	A	alt_assembly_8	HuRef	HuRef	view	507
3	NW_921807.1	42509826	134324156	plus	T	alt_assembly_1	Celera	Celera	view	507
3	NT_005612.15	42394130	137381674	plus	T	ref_assembly	reference	reference	view	507

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005612

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC092991.12 NC_000003.10	AC026969.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10056691	HapMap-CEU	European	120	IG	0.050	0.283	0.667	0.371	0.192	0.808

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	90	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.150	0.833	0.479	0.092	0.908

ss24317471	AFD_EUR_PANEL	European	48	IG	0.083	0.292	0.625	0.403	0.229	0.771

	AFD_AFR_PANEL	African American	42	IG		0.190	0.810	0.655	0.095	0.905

	AFD_CHN_PANEL	Asian	48	IG			1.000			1.000

ss66116249	HapMap-CEU	European	118	GF	0.017	0.288	0.695		0.161	0.839

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF		0.022	0.978		0.011	0.989

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.133	0.850		0.083	0.917

ss68876385	HapMap-CEU	European	120	GF	0.050	0.283	0.667		0.192	0.808

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.150	0.833		0.092	0.908

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss10056691	263	2	36	225
ss24317471	71	2	11	56
ss66116249	262	2	36	224
ss68876385	263	2	36	225

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs6786582	332	4	45	274

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
255	ss10056691	C/C	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r23_ch3_CEU_affymetrix:genechip500k	389849
255	ss66116249	C/T	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	chr3-HapMap-CEU
255	ss68876385	C/C	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	chr3-HapMap-CEU
262	ss10056691	C/T	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r23_ch3_CEU_affymetrix:genechip500k	389849
262	ss66116249	T/T	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	chr3-HapMap-CEU
262	ss68876385	C/T	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	chr3-HapMap-CEU
264	ss10056691	C/C	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	r23_ch3_CEU_affymetrix:genechip500k	389849
264	ss66116249	C/T	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	chr3-HapMap-CEU
264	ss68876385	C/C	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	chr3-HapMap-CEU
360	ss10056691	C/C	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	r23_ch3_CEU_affymetrix:genechip500k	389849
360	ss66116249	C/T	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	chr3-HapMap-CEU
360	ss68876385	C/C	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	chr3-HapMap-CEU
620	ss10056691	C/T	CSHL-HAPMAP	HapMap-CEU	NA12874	CEPH1459.11	r23_ch3_CEU_affymetrix:genechip500k	389849
620	ss66116249	T/T	CSHL-HAPMAP	HapMap-CEU	NA12874	CEPH1459.11	chr3-HapMap-CEU
620	ss68876385	C/T	CSHL-HAPMAP	HapMap-CEU	NA12874	CEPH1459.11	chr3-HapMap-CEU
5198	ss10056691	T/T	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	r23_ch3_JPT_affymetrix:genechip500k	389849
5198	ss66116249	C/T	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	chr3-HapMap-JPT
5198	ss68876385	T/T	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	chr3-HapMap-JPT
5309	ss10056691	C/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	r23_ch3_YRI_affymetrix:genechip500k	389849
5309	ss66116249	T/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	chr3-HapMap-YRI
5309	ss68876385	C/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	chr3-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .