Reference SNP(refSNP) Cluster Report: rs7741

Reference SNP(refSNP) Cluster Report: rs7741

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/130
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_003739.4:c.90G>A
NT_077567.3:g.5078607G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss61706505 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7741 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	Ancestral Allele	Success Rate
ss9656	CGAP-GAI\|50485	fwd/T	A/G	atttggcacctatgcacctccagaggttcc	agaagtaaagctttggaggtcacaaaatta	08/23/99	10/25/06	52	cDNA		99 %
ss20260	UWGC\|2200	fwd/T	A/G	atttggcacctatgcacctccagaggttcc	agaagtaaagctttggaggtcacaaaatta	11/15/99	12/23/03	85	Genomic		unknown
ss1524962	LEE\|402023	fwd/T	A/G	atttggcacctatgcacctccagaggttcc	agaagtaaagctttggaggtcacaaaatta	09/13/00	10/10/03	102	cDNA		unknown
ss4415684	LEE\|e402023	fwd/T	A/G	atttggcacctatgcacctccagaggttcc	agaagtaaagctttggaggtcacaaaatta	04/26/02	10/10/03	108	cDNA		unknown
ss16252225	CGAP-GAI\|1503797	fwd/T	A/G	atttggcacctatgcacctccagaggttcc	agaagtaaagctttggaggtcacaaaatta	11/18/03	11/22/03	130	cDNA		unknown
ss18885412	SC_SNP\|SC-CHR9-12_NA07340-200402.chr10.NT_077567.3_5078607	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	02/20/04	03/04/04	126	Genomic		unknown
ss23561097	PERLEGEN\|afd2201843	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	08/10/04	09/13/04	126	Genomic		unknown
ss24780242	SEQUENOM\|sqnm5768	rev/B	C/T	taantttgtgacctncaaagctttacttct	ggaacctctggaggtgcataggtgccaaat	06/18/04	06/18/04	130	cDNA		unknown
ss24789834	SEQUENOM\|sqnm92806	rev/B	C/T	taantttgtgacctncaaagctttacttct	ggaacctctggaggtgcataggtgccaaat	06/18/04	06/18/04	130	cDNA		unknown
ss28503785	MGC_GENOME_DIFF\|BC001479x37551026-G5078607A	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	08/25/04	08/25/04	126	cDNA		unknown
ss38343013	CEPH\|G9-SN-E2S3	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	05/19/05	05/19/05	125	Genomic	G	100 %
ss38511264	ABI\|hCV1844834	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	07/15/05	07/15/05	126	Genomic		unknown
ss61706505	SI_EXO\|NT_077567.3_5078607	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	07/11/06	08/14/07	127	Genomic		unknown
ss66498423	AFFY\|SNP_A-4202197	fwd/T	A/G	tgctcctccaggttcc	agaagtaaagctttgg	10/29/06	08/14/07	127	Genomic		unknown
ss76321351	AFFY\|AFFY_6_1M_SNP_A-4202197	fwd/T	A/G	tgctcctccaggttcc	agaagtaaagctttgg	08/28/07	08/30/07	129	Genomic		unknown
ss77778496	HGSV\|Cor12156_SNV_20070510.chr10_5128607	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	10/09/07	10/14/07	129	Genomic		unknown
ss81404281	KRIBB_YJKIM\|KHS30466	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	11/30/07	11/30/07	130	Genomic		unknown
ss86240941	CORNELL\|hCV1844834	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	01/21/08	01/21/08	129	Genomic		unknown
ss88076328	BCMHGSC_JDW\|JWB-0227557	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	02/26/08	02/27/08	129	Genomic		unknown
ss97617117	HUMANGENOME_JCVI\|1103649847823	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	03/29/08	03/29/08	130	Genomic		unknown
ss105439130	SNP500CANCER\|AKR1C3-27	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttgkaggtcacaaartta	09/05/08	09/05/08	130	Genomic		unknown
ss109186326	1000GENOMES\|CEU.trio.12.15.2008_2283489_chr10_5128607	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	12/15/08	12/16/08	130	Genomic		unknown
ss118996717	ILLUMINA-UK\|NA18507_000008645_NCBI36.1_chr10_5128607	fwd/T	A/G	atactacctttggttgctcctccaggttcc	agaagtaaagctttggaggtcacaaaatta	01/21/09	01/22/09	130	Genomic		99 %

Fasta sequence (Legend)

 CATTCTGTGT AATATCACTG GGAGAGAACT CATATGAGCT TGCACCGTTT CCCTTCTATA
 CTCCATGTGA TTTTTACCAT GTATAATATC ACTATATTAA AAATAATTAG GACTATTTCA
 GTCATGTTAA CTTTTCCAAC AAATCACTGA ATCTGAGGGT GTTATTTGGT ACCTCCATAA
 CAGTGATCAA CCAGAGATTG CCTGAGACTG AAGGTGTTTC TGGGATGCTC AACCTTTATT
 ACTAACCAGG AAAGACTCAG GCAAACTGAG ATGGACTTTT CACCCCACAT ACAGACAGGA
 GGAAAAGCTG ATTCTTGTAT AAAAGTCAAT GCTTGTGCCT GAACTACCTC TCAGCCACAG
 TGATCACCAG ATACTACCTT TGGTTGCTCC TCCAGGTTCC
 R
 AGAAGTAAAG CTTTGGAGGT CACAAAATTA GCAATAGAAG CTGGGTTCCG CCATATAGAT
 TCTGCTCATT TATACAATAA TGAGGAGCAG GTTGGACTGG CCATCCGAAG CAAGATTGCA
 GATGGCAGTG TGAAGAGAGA AGACATATTC TACACTTCAA AGGTACTGTG TCTATGATGA
 GCTTGTGTGC ACATGTATTT ATTGTGATTG TGTGGAGATG ACAATTCTAT GACTGGATGA
 GTAGTTGTGG GTGAATTTTG CTTCTGGGTT CAAATTTATT CACACATACT CACATACTAA
 AACTGAAATC AAAATCAAGG AATGATGATC ACTTTTCATT TTGGCTGTGT TCCAATTTAT
 GACCTGAAAG TCCCTTTACT TTTTTGAGCT TCAGCTGAGA

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
dbSTS	GenBank
G62081 sqnm5768 sqnm92806	S68288 ABBA01035203 BC001479 BG547635 Hs.78183 NM_003739

dbSNP Blast Analysis

UniGene Cluster ID
78183

3D structure mapping
NP_003730

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss105439130	P1		204	GF	0.098	0.373	0.529		0.284	0.716

	CAUC1		62	GF	0.194	0.516	0.290		0.452	0.548

	AFR1		48	GF	0.125	0.500	0.375		0.375	0.625

	HISP1		46	GF		0.435	0.565		0.217	0.783

	PAC1		48	GF	0.042		0.958		0.042	0.958

	P3		560	GF	0.046	0.275	0.679		0.184	0.816

	CAUC3		132	GF	0.091	0.439	0.470		0.311	0.689

	AFR3		152	GF	0.039	0.395	0.566		0.237	0.763

	HISP3		98	GF		0.082	0.918		0.041	0.959

	PAC3		178	GF	0.045	0.157	0.798		0.124	0.876

ss23561097	AFD_EUR_PANEL	European	48	IG	0.042	0.583	0.375	0.150	0.333	0.667

	AFD_AFR_PANEL	African American	46	IG	0.174	0.565	0.261	0.527	0.457	0.543

	AFD_CHN_PANEL	Asian	48	IG			1.000			1.000

ss61706505	HapMap-CEU	European	118	IG	0.153	0.475	0.373		0.390	0.610

	HapMap-HCB	Asian	88	IG			1.000			1.000

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	0.169	0.356	0.475		0.347	0.653

ss66498423	HapMap-CEU	European	118	GF	0.153	0.475	0.373		0.390	0.610

	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	0.167	0.350	0.483		0.342	0.658

ss76321351	ICMHP		6	IG			1.000			1.000

ss9656	COHORT_CONSORTIUM_B		76	AF					0.342	0.658

	COHORT_CONSORTIUM_C		76	AF					0.395	0.605

	COHORT_CONSORTIUM_H		76	AF					0.097	0.903

	COHORT_CONSORTIUM_J		76	AF					0.027	0.973

	COHORT_CONSORTIUM_L		76	AF					0.186	0.814

	CEPH-TRIOS		606	AF					0.363	0.637

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.335+/-0.235	1183	967	275	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	YES	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .