Reference SNP(refSNP) Cluster Report: rs2841280

Reference SNP(refSNP) Cluster Report: rs2841280

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/130
Map to Genome Build:	36.3

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

HGVS Names
NM_138790.2:c.79G>C
NP_620145.2:p.Glu27Gln
NT_026437.11:g.86394601G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43666287 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2841280 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
ss4022991	SC_JCM\|AL583810.2_89106	fwd/T	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacggtaggactggggggcccca	09/26/01	10/10/03	100	Genomic	unknown
ss16239349	CGAP-GAI\|1475679	fwd/T	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacgttgcaggtcctgggagcgc	11/18/03	11/22/03	126	cDNA	unknown
ss21215320	SSAHASNP\|WGSA-200403-chr14.chr14.NT_026437.10_85295232	fwd/T	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacggtaggactggggggcccca	03/19/04	03/19/04	121	Genomic	unknown
ss43666287	ABI\|hCV9228797	fwd/	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacggtaggactggggggcccca	07/18/05	08/14/07	126	Genomic	unknown
ss69169757	PERLEGEN\|PGP04766377	fwd/	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacggtaggactggggggcccca	01/30/07	08/14/07	127	Genomic	unknown
ss86272753	CORNELL\|hCV9228797	fwd/	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacggtaggactggggggcccca	01/21/08	01/21/08	129	Genomic	unknown
ss96885391	HUMANGENOME_JCVI\|1103649153269	fwd/	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacggtaggactggggggcccca	03/27/08	03/27/08	130	Genomic	unknown
ss118798279	ILLUMINA-UK\|NA18507_000110904_NCBI36.1_chr14_104464601	fwd/	C/G	tccatgccgccccgccgcccgtgggacaga	aggctggcacggtaggactggggggcccca	01/21/09	01/22/09	130	Genomic	99 %

Fasta sequence (Legend)

 GGTGACATGT GGCCGGCTGC GGGCTCCAAC ACCCACACGG CTTGTCCTCG TGGAAAGCAC
 ACCCCCAACA TCCAGGGCGT GACCTCGGGC ATGAGTGGGG GGCTTTTGGG GGCTTATGTG
 GGTGTCTGTG CAGGGGTGTC CCCAGTGCCC AGCTGCCCAG GCACTGAGGG GCAGTTCTGG
 GCAGAGCTGG AGCTGCTGGT GATGCCAGGC TGCCCTGTGC AGATGCTGAA GCCTCTTTGG
 AAAGCAGCAG TGGCCCCCAC ATGGCCATGC TCCATGCCGC CCCGCCGCCC GTGGGACAGA
 S
 AGGCTGGCAC GGTAGGACTG GGGGGCCCCA GGGGGGAGGT GGCTGGGATC AATGGCCTTT
 CAAGAGCTCC GAGCCAGAGT GGAGAGGTCA CAAGCAGCCT TGAGGGGGCC TCCAAGCAGA
 GGTGCCCTGA CTGGTGGGCA AGGGAAGCCT CCCTGGGCTG CTCCAGACCT TCCCTTTATG
 CCCCTGCTGG AGGTGCTGGG GACAGCCAGT TACCACGAGC CACAGCATTG CAGAGTGGGC
 TGCAGGCCCC CTGACCCCTG CCACCACCCT GGGCTGGGGG CCTTCTCTGT ATCACCCTCC

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
GenBank
NT_026437 ABBA01008850 AC013648 AL512802 BM809062

dbSNP Blast Analysis

UniGene Cluster ID
407101

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss43666287	HapMap-CEU	European	100	IG	0.280	0.580	0.140		0.570	0.430

	HapMap-YRI	Sub-Saharan African	102	IG	0.020	0.471	0.510		0.255	0.745

ss69169757	HapMap-CEU	European	118	GF		1.000			0.500	0.500

	HapMap-HCB	Asian	90	GF		1.000			0.500	0.500

	HapMap-JPT	Asian	90	GF		1.000			0.500	0.500

	HapMap-YRI	Sub-Saharan African	120	GF		1.000			0.500	0.500

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss43666287	278		74
ss96885391	1	1

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs2841280	351	1	74

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
158	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12145	CEPH1334.11	r27_ch14_CEU_bcm:genotype_0002
159	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	r27_ch14_CEU_bcm:genotype_0002
169	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	r27_ch14_CEU_bcm:genotype_0002
171	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	r27_ch14_CEU_bcm:genotype_0002
175	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	r27_ch14_CEU_bcm:genotype_0002
187	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA06985	CEPH1341.14	r27_ch14_CEU_bcm:genotype_0002
200	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r27_ch14_CEU_bcm:genotype_0002
203	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA07348	CEPH1345.02	r27_ch14_CEU_bcm:genotype_0002
238	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA11881	CEPH1347.14	r27_ch14_CEU_bcm:genotype_0002
253	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA11840	CEPH1349.14	r27_ch14_CEU_bcm:genotype_0002
254	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA10856	CEPH1350.01	r27_ch14_CEU_bcm:genotype_0002
264	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	r27_ch14_CEU_bcm:genotype_0002
363	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA11995	CEPH1362.16	r27_ch14_CEU_bcm:genotype_0002
366	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA10863	CEPH1375.02	r27_ch14_CEU_bcm:genotype_0002
409	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12236	CEPH1408.11	r27_ch14_CEU_bcm:genotype_0002
410	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12155	CEPH1408.12	r27_ch14_CEU_bcm:genotype_0002
438	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12248	CEPH1416.11	r27_ch14_CEU_bcm:genotype_0002
456	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA10838	CEPH1420.01	r27_ch14_CEU_bcm:genotype_0002
457	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA10839	CEPH1420.02	r27_ch14_CEU_bcm:genotype_0002
465	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12004	CEPH1420.10	r27_ch14_CEU_bcm:genotype_0002
536	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch14_CEU_bcm:genotype_0002
545	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	r27_ch14_CEU_bcm:genotype_0002
548	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch14_CEU_bcm:genotype_0002
565	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	r27_ch14_CEU_bcm:genotype_0002
579	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12815	CEPH1454.15	r27_ch14_CEU_bcm:genotype_0002
618	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12872	CEPH1459.09	r27_ch14_CEU_bcm:genotype_0002
619	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12873	CEPH1459.10	r27_ch14_CEU_bcm:genotype_0002
621	ss43666287	C/C	CSHL-HAPMAP	HapMap-CEU	NA12875	CEPH1459.12	r27_ch14_CEU_bcm:genotype_0002
623	ss43666287	G/G	CSHL-HAPMAP	HapMap-CEU	NA12878	CEPH1463.02	r27_ch14_CEU_bcm:genotype_0002
5134	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	r27_ch14_YRI_bcm:genotype_0002
5136	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19132	YOR101.01	r27_ch14_YRI_bcm:genotype_0002
5137	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	r27_ch14_YRI_bcm:genotype_0002
5138	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19130	YOR101.03	r27_ch14_YRI_bcm:genotype_0002
5139	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r27_ch14_YRI_bcm:genotype_0002
5142	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r27_ch14_YRI_bcm:genotype_0002
5144	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r27_ch14_YRI_bcm:genotype_0002
5145	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19240	YOR117.01	r27_ch14_YRI_bcm:genotype_0002
5147	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19239	YOR117.03	r27_ch14_YRI_bcm:genotype_0002
5244	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	r27_ch14_YRI_bcm:genotype_0002
5245	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	r27_ch14_YRI_bcm:genotype_0002
5246	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18859	YOR012.03	r27_ch14_YRI_bcm:genotype_0002
5247	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18515	YOR013.01	r27_ch14_YRI_bcm:genotype_0002
5252	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	r27_ch14_YRI_bcm:genotype_0002
5253	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	r27_ch14_YRI_bcm:genotype_0002
5255	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18871	YOR017.03	r27_ch14_YRI_bcm:genotype_0002
5256	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	r27_ch14_YRI_bcm:genotype_0002
5258	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18853	YOR018.03	r27_ch14_YRI_bcm:genotype_0002
5260	ss43666287	C/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r27_ch14_YRI_bcm:genotype_0002
5261	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	r27_ch14_YRI_bcm:genotype_0002
5264	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	r27_ch14_YRI_bcm:genotype_0002
5267	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r27_ch14_YRI_bcm:genotype_0002
5268	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	r27_ch14_YRI_bcm:genotype_0002
5272	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	r27_ch14_YRI_bcm:genotype_0002
5274	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	r27_ch14_YRI_bcm:genotype_0002
5275	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r27_ch14_YRI_bcm:genotype_0002
5276	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	r27_ch14_YRI_bcm:genotype_0002
5277	ss43666287	C/C	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r27_ch14_YRI_bcm:genotype_0002
5283	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19205	YOR048.01	r27_ch14_YRI_bcm:genotype_0002
5284	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19204	YOR048.02	r27_ch14_YRI_bcm:genotype_0002
5285	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	r27_ch14_YRI_bcm:genotype_0002
5287	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r27_ch14_YRI_bcm:genotype_0002
5288	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19210	YOR050.03	r27_ch14_YRI_bcm:genotype_0002
5293	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r27_ch14_YRI_bcm:genotype_0002
5294	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r27_ch14_YRI_bcm:genotype_0002
5295	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r27_ch14_YRI_bcm:genotype_0002
5297	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	r27_ch14_YRI_bcm:genotype_0002
5298	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19120	YOR060.01	r27_ch14_YRI_bcm:genotype_0002
5299	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19116	YOR060.02	r27_ch14_YRI_bcm:genotype_0002
5300	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19119	YOR060.03	r27_ch14_YRI_bcm:genotype_0002
5304	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19154	YOR072.01	r27_ch14_YRI_bcm:genotype_0002
5306	ss43666287	G/G	CSHL-HAPMAP	HapMap-YRI	NA19153	YOR072.03	r27_ch14_YRI_bcm:genotype_0002
5307	ss43666287	C/C	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r27_ch14_YRI_bcm:genotype_0002

Genotype data submitted for	351	samples from	351	individuals	Individual with multiple genotypes submission:	0

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 .