Reference SNP(refSNP) Cluster Report: rs84933

Reference SNP(refSNP) Cluster Report: rs84933

refSNP ID: rs84933
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001498.2:c.560+517C>T
NT_007592.14:g.44238621G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss91378 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs84933 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
ss91378	TSC-CSHL\|TSC0111981	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	09/06/00	04/07/04	92	Genomic	95 %
ss851771	SC_JCM\|AL157773.5_14160	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	07/27/00	10/10/03	83	Genomic	unknown
ss986939	KWOK\|OVLP-000804-617781	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	09/01/00	10/10/03	87	Genomic	99 %
ss1046623	KWOK\|OVLP-000804-619663	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	09/02/00	10/10/03	87	Genomic	97 %
ss2991918	YUSUKE\|IMS-JST004690	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	05/24/01	10/25/06	96	Genomic	unknown
ss3185246	HGBASE\|SNP000570830	rev/B	C/T	taagttgctttaaggctctcactag	ctgatcttagctttgtacaatgcat	07/09/01	10/10/03	98	Genomic	unknown
ss5521908	TSC-CSHL\|TSC0535472	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	09/21/02	10/10/03	108	Genomic	unknown
ss6042454	SC_JCM\|NT_007592.10_44183167	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	01/10/03	10/10/03	111	Genomic	unknown
ss10332071	BCM_SSAHASNP\|chr6.NT_007592.13_44177498	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	06/29/03	10/10/03	116	Genomic	unknown
ss13106481	SC_SNP\|NT_007592.13_44177498	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	10/22/03	10/31/03	119	Genomic	unknown
ss19690888	CSHL-HAPMAP\|CSHL-HuDD-200402.chr6.NT_007592.13_44177498	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	02/20/04	03/04/04	120	Genomic	unknown
ss22484099	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007592.13_44177498	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	03/21/04	03/21/04	121	Genomic	unknown
ss23973294	PERLEGEN\|afd0315793	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	08/10/04	09/13/04	123	Genomic	unknown
ss28529553	EGP_SNPS\|GCLC-031440	rev/B	C/T	ggttttaagttgctttaaggctctcactag	ctgatcttagctttgtacaatgcatgctca	11/08/04	01/27/05	126	Genomic	unknown
ss44746662	ABI\|hCV8910681	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	07/19/05	11/03/06	126	Genomic	unknown
ss93462152	BCMHGSC_JDW\|JWB-2141398	fwd/T	A/G	tgagcatgcattgtacaaagctaagatcag	ctagtgagagccttaaagcaacttaaaacc	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATTATTTTTA TTTTCCTTTA AACACATGAC AACATATGAA GTTAGAAACT ACGTCTACAA
 ATATCTGTCT TCCCCAAAAG GCTCTGCACA TAGCAAACGT GAGGGCCTGT TAAAGGAATG
 AACGCTGAGA AGTCTCCATG TTCCCACTCT GGATCAGGAG CCTAGGCTCA GGATGACAGA
 TGAGCATGCA TTGTACAAAG CTAAGATCAG
 R
 CTAGTGAGAG CCTTAAAGCA ACTTAAAACC TCAGAATTGA ACAACAAACC AACAGAACTT
 GAAGTTAATG GAAGAGAGTG CCTATTATAT ATATCAGGTA CTGCACCTAT TTTATAAGTT
 ATATAGAGTA AGATGGGCAA ATCACAGATA CTGATGGTTA GAGAGGACAA AAAAGGAGAA
 ATAACTAAGA GAAAAAAAAA ATCCCAGTAG GCATTTACAG ACCTAGGACT GAAAATAATC
 TCCCTATTAA AAGAGTTATT CGCAGTGGCT CAGCGAATAA CTTTGTGACG ACTTGGAGAA
 TTGACAAATC AAGCCTGGTG CATGCATCAA CAACCAAAAA GCCTGGGGGT ACTGAAGATG
 TGAACAGGTG CACATCTGCT ATCTTCTCTG GTTACTTAGG AAGAGAGCCA AAACTCAGTT
 AATGCTCAAA AAGGATTTCT AGACAGAAAT ACTATACTCT CATAAGTCAA GGGTCTAGTG
 AAGGGCATCT GCATTTCAAC ACAAAACCAT ACTCACCTGA AGCGAGGGGG CTTTGTTTAT
 TGCTTCATCT GGAAAAAAAG GGACTTGAAG CTCCTCCTTT CACTGGGTTG GGTTTGACCT
 CGGGCAGTGT GAACCCAGAC AGCCTTATCT ACACAAATT

GeneView

GeneView via analysis of contig annotation: GCLC glutamate-cysteine ligase, catalytic subunit

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_007592->NM_001498

function

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


reference	NT_007592->NM_001498->NP_001489	44238621	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs84933 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838981.2	4055924	53211974	minus	C	alt_assembly_8	HuRef	HuRef	view	210
6	NT_007592.14	44238621	53488349	plus	G	ref_assembly	reference	reference	view	210
6	NW_923073.1	26506873	55042552	plus	G	alt_assembly_1	Celera	Celera	view	210

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592.10 AL033397 AL033397.7 AL157773.10

dbSNP Blast Analysis
GenBank HTGS Finished:
AL033397.7

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23973294	AFD_EUR_PANEL	European	46	IG	0.217	0.391	0.391	0.371	0.413	0.587

	AFD_AFR_PANEL	African American	46	IG	0.174	0.304	0.522	0.150	0.326	0.674

	AFD_CHN_PANEL	Asian	48	IG	0.167	0.500	0.333	1.000	0.417	0.583

ss28529553	PDR90	Global	176	IG	0.205	0.489	0.307	1.000	0.449	0.551

ss2991918	JBIC-allele		1470	AF					0.457	0.543

ss44746662	AoD_African_American		90	AF					0.440	0.560

	AoD_Caucasian		92	AF					0.400	0.600

	AoD_Chinese		90	AF					0.370	0.630

	AoD_Japanese		90	AF					0.560	0.440

ss91378	TSC_42_AA		80	AF					0.390	0.610

	TSC_42_C		58	AF					0.330	0.670

	TSC_42_A		72	AF					0.400	0.600

	HapMap-CEU	European	120	IG	0.217	0.583	0.200	0.200	0.508	0.492

	HapMap-HCB	Asian	90	IG	0.222	0.444	0.333	0.527	0.444	0.556

	HapMap-JPT	Asian	90	IG	0.200	0.511	0.289		0.456	0.544

	HapMap-YRI	Sub-Saharan African	120	IG	0.067	0.467	0.467	0.403	0.300	0.700