Reference SNP(refSNP) Cluster Report: rs2979494

Reference SNP(refSNP) Cluster Report: rs2979494

refSNP ID: rs2979494
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	101/129
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_002095.4:c.258+4392T>C
NT_007995.14:g.808931A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10435080 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2979494 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
ss4193630	SC_JCM\|AF252826.3_109265	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	10/15/01	10/10/03	101	Genomic	unknown
ss10435080	BCM_SSAHASNP\|chr8.NT_007995.13_808931	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	06/29/03	05/17/04	116	Genomic	unknown
ss17959269	CSHL-HAPMAP\|CSHL-HuCC-200402.chr8.NT_007995.13_808931	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	02/19/04	03/04/04	120	Genomic	unknown
ss22707095	SSAHASNP\|WGSA-200403-chr8.chr8.NT_007995.13_808931	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	03/21/04	03/21/04	121	Genomic	unknown
ss24223345	PERLEGEN\|afd4087755	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	08/10/04	09/13/04	123	Genomic	unknown
ss69046046	PERLEGEN\|PGP04087755	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	01/30/07	03/31/08	127	Genomic	unknown
ss80609240	HGSV\|Cor18507_SNV_20070510.chr8_30607699	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	11/23/07	11/26/07	130	Genomic	unknown
ss86119806	HGSV\|Cor18517_SNV_20070510.chr8_30607699	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	12/06/07	12/11/07	130	Genomic	unknown
ss93864517	BCMHGSC_JDW\|JWB-2448700	fwd/T	A/G	cacctccccccgccatgaaaaagtaatctc	cctccattcagaatttgtgatgcagagcct	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 AACAGTTTCC CTATTAAATG AATCAACTAT AAGGAGCATT TCTGTTGCCT TTCTTTTGCT
 TTCTTTCTAA AGGTACACAA AAGACAGTGG GAGACTTTCC AAGAATCTGT TTACAGATAC
 CTTCCAAATG TACTTCTTCC CTTTCAAAAT AAGCCCTTCT CTTTACCTTC CACCTCCCCC
 CGCCATGAAA AAGTAATCTC
 R
 CCTCCATTCA GAATTTGTGA TGCAGAGCCT GAAGGAATAA TAAACTCCAG GGACCCAAAC
 AAACAGACAA GCCAAAAAAA TGGTTTCAGG GAAGCATTCG TGAATGGTAA CTGAGGTGCC
 GTAAACTATC CATTACTGGG CTTCTTGTCT TTTCCAGTCA CATATTTTTC AAAGAGTTTA
 AAAtattttg gcccctgctg gaacattcta atctatcata atctgtgagc aattgtttaa
 agtttcctct aacaaccatt ccccctacac ccccacctcc attcagtatt gtccaagaac
 gcattgctct taggggacag tatgataaaa gtaatgcaca gagaacactg gttaaaaaaa
 agataaaaag aaatattttt ttcaagaatt cttatttttt tattagcgac aaggtctcaa
 tgtgtcgccc aggctggagt acagtggtgc aatcttggct cattgcaact tccacctccc
 aggctcatgt gattctcagc ctctaaagta gctgcggtta caggcatgtg ccaacacacc
 tggttaattt ctttttgtat ttttagtaga gacggggttt caccatgttg gccaggctgg
 tctcaaactc aagtgatcca cctgcctcag cctcccaaag cgctgagaat acaggtgtga
 gccactgtgc tgggccgaga atttaaatat aagtaattct caaaactcat tccctgaata
 tttattagct tgaagaaaaa gcatatttag agagctggaa caatatcaat tagggaggct
 gattccttta aatataaaag aaatactttc taggactgcc aagtcattca aattgtgcta
 tataaaagct gtatagaaat tactttagat tgagtgtgca ttactcaata tggtagttaa
 aatctatttt gtcaaatcgt atcattaaag ttttattcta attagtcaat tctcattata
 gtttttcaac agtttaatat ttctaccttc tactgacaaa aaataagata tgctagctgt
 catactgagt agtttgaagc agtaggtatc tctttcatta attacCCAAA TAAAAATGTA
 AGGTTACTTC TGATTCATTC CCTTTTATTT ATACCTAATA GCTGAGATCA GAGATCAGAA
 GATGCAGGAA CACACATTTA AAAAGGAGTA ACAggccagg tctagtggct cacgcctgta
 atcccagcac ttcaggaggc tgaggcaggc ggatcacttg agggatcccc tgagcccagg
 agttcaagac caagctgggc aacactgaga gaccctgtct ctacaaaaaa aatacaaaaa
 ttagccaggc atggtggcac gtgcctgtag tcccagttac ttgggaggtt gaggtgggag
 gatcacttga ggctaggaga tcgaggctgc agtgagccag gatggtgcca atgcactcta
 gcctaggtga cagagttaag accctgtctc aaaaacaaat aaataaataa aGGAATAACA
 CAACTTTTAT CATATCCCTT GCTTCATATT TTAACTgatT TAATTTTTAA TCTAACATGA
 CAAG

GeneView

GeneView via analysis of contig annotation: GTF2E2 general transcription factor IIE, polypeptide 2, beta 34kDa

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_007995->NM_002095

function

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


reference	NT_007995->NM_002095->NP_002086	808931	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2979494 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_001839128.2	8278313	29032693	minus	C	alt_assembly_8	HuRef	HuRef	view	200
8	NW_923907.1	18014512	29446674	plus	G	alt_assembly_1	Celera	Celera	view	200
8	NT_007995.14	808931	30607699	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007995 AF215848

dbSNP Blast Analysis
GenBank HTGS Draft:
AF215848.3 AF252826.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss10435080	HapMap-CEU	European	120	IG		0.367	0.633	0.100	0.183	0.817

	HapMap-HCB	Asian	88	IG	0.409	0.364	0.227	0.150	0.591	0.409

	HapMap-JPT	Asian	88	IG	0.136	0.591	0.273	0.200	0.432	0.568

	HapMap-YRI	Sub-Saharan African	120	IG	0.067	0.300	0.633	0.371	0.217	0.783

	CHMJ	Asian	74	IG					0.432	0.568

ss24223345	AFD_EUR_PANEL	European	48	IG	0.125	0.208	0.667	0.050	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	0.167	0.500	0.333	1.000	0.417	0.583

ss69046046	HapMap-CEU	European	120	GF		0.367	0.633		0.183	0.817

	HapMap-HCB	Asian	90	GF	0.400	0.378	0.222		0.589	0.411

	HapMap-JPT	Asian	90	GF	0.133	0.600	0.267		0.433	0.567

	HapMap-YRI	Sub-Saharan African	120	GF	0.067	0.133	0.800		0.133	0.867

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss10435080	254	32	82	138
ss24223345	71	7	21	41
ss69046046	254	32	84	138

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs2979494	332	38	104	172

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5139	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5139	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	chr8-HapMap-YRI
5144	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5144	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	chr8-HapMap-YRI
5238	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5238	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	chr8-HapMap-YRI
5239	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA18505	YOR005.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5239	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA18505	YOR005.02	chr8-HapMap-YRI
5241	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5241	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	chr8-HapMap-YRI
5242	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA18508	YOR009.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5242	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA18508	YOR009.02	chr8-HapMap-YRI
5251	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5251	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	chr8-HapMap-YRI
5259	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5259	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr8-HapMap-YRI
5266	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA18912	YOR028.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5266	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA18912	YOR028.02	chr8-HapMap-YRI
5272	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5272	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	chr8-HapMap-YRI
5283	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19205	YOR048.01	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5283	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19205	YOR048.01	chr8-HapMap-YRI
5285	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5285	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	chr8-HapMap-YRI
5290	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5290	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	chr8-HapMap-YRI
5293	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5293	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	chr8-HapMap-YRI
5296	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19222	YOR058.02	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5296	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19222	YOR058.02	chr8-HapMap-YRI
5301	ss10435080	A/G	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	r23_ch8_YRI_illumina:golden_gate_1.0.0	599719
5301	ss69046046	G/G	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	chr8-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 .