Reference SNP(refSNP) Cluster Report: rs4072677

Reference SNP(refSNP) Cluster Report: rs4072677

refSNP ID: rs4072677
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
Map to Genome Build:	36.3

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

HGVS Names
NM_004759.3:c.279+20269G>T
NM_032960.2:c.279+20269G>T
NT_021877.18:g.396901G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5451882 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4072677 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
ss5451882	TSC-CSHL\|TSC0122493	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	09/21/02	10/25/06	108	Genomic	unknown
ss6303106	SC_JCM\|NT_021877.12_342229	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	01/10/03	10/10/03	111	Genomic	unknown
ss9893096	BCM_SSAHASNP\|chr1.NT_021877.15_342229	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	06/27/03	10/10/03	116	Genomic	unknown
ss16388619	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_021877.16_342229	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	02/17/04	03/04/04	120	Genomic	unknown
ss19098651	CSHL-HAPMAP\|CSHL-HuDD-200402.chr1.NT_021877.16_342229	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	02/20/04	03/04/04	120	Genomic	unknown
ss19831974	CSHL-HAPMAP\|CSHL-HuFF-200402.chr1.NT_021877.16_342229	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	02/21/04	03/04/04	120	Genomic	unknown
ss20471001	SSAHASNP\|WGSA-200403-chr1.chr1.NT_021877.16_342229	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	03/18/04	03/18/04	121	Genomic	unknown
ss23703558	PERLEGEN\|afd1167023	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	08/10/04	09/13/04	123	Genomic	unknown
ss44018879	ABI\|hCV26593147	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	07/18/05	07/18/05	126	Genomic	unknown
ss68790610	PERLEGEN\|PGP01167023	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	01/30/07	03/31/08	127	Genomic	unknown
ss85252048	HGSV\|Cor19129_SNV_20070510.chr1_203267517	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	12/06/07	12/08/07	130	Genomic	unknown
ss87947625	BCMHGSC_JDW\|JWB-0176307	fwd/B	G/T	cagaattgtgaactggatttatggaagttt	tggagtttgaaaattcgagagtcctggctg	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTGCTTGCTA ATCCTGGAAG CAGAGGGGAA CAAGATTTAG CTCCCTTATC TCTCTGCCTT
 CTCCTTTCCG ATGGGTGCAA TTGTGTTGAC TCTTGAGGGA CAGCCAGGAA GAAGCAGGTG
 GGCTGGATGC TTTCTCCTTT CTCCACCAAC CCAAGGGCAT CTGGAGGGTG GACCAGGGCA
 GAAAGGCGAT TAGCTCTCCG TTACCCAGGG AGCTGAGACA AAGGCATTTT GGGTTAAATT
 CAAGGAGGAA TTCAGAATTG TGAACTGGAT TTATGGAAGT TT
 K
 TGGAGTTTGA AAATTCGAGA GTCCTGGCTG GACTTGTGCT TGGAACGTTG GTCGGAGGTG
 GATATGAATG ATGGGTCCTG CAGATGGCCG ACTCCTGAGA AATGACTGGG AGGCTTTACT
 GGATTTTTCG CTTGGAACAA ACCCAAGCTT AGGGAATTCC CGGAGCCTGT TGCAGGCCTC
 AACACCCTTC TGGTGCAGCT TCGCTGTGAG GCAGTGGTTA TTTCTCAGGA AACTGGCAAC
 TGGGAGTAAA TGGGAGTGTG GGGTGGGAAT CAGCTACTCT TCCTGAGGAT TATACACTTC
 CAGTGTAATT AAGGCGGGGT CAGGATCTCC TATCTCttat ttatttattt atttatttat
 ttatttattt atttatttat ttgcttaATC

GeneView

GeneView via analysis of contig annotation: MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2

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_021877->NM_004759

function

reference

NT_021877->NM_032960

function

HuRef

NW_001838536->NM_004759

function

HuRef

NW_001838536->NM_032960

function

Celera

NW_926794->NM_004759

function

Celera

NW_926794->NM_032960

function

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


reference	NT_021877->NM_004759->NP_004750	396901	forward	intron

reference	NT_021877->NM_032960->NP_116584	396901	forward	intron

HuRef	NW_001838536->NM_004759->NP_004750	310238	forward	intron

HuRef	NW_001838536->NM_032960->NP_116584	310238	forward	intron

Celera	NW_926794->NM_004759->NP_004750	296319	forward	intron

Celera	NW_926794->NM_032960->NP_116584	296319	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4072677 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838536.1	310238	177577434	plus	T	alt_assembly_8	HuRef	HuRef	view	282
1	NW_926794.1	296319	180130559	plus	G	alt_assembly_1	Celera	Celera	view	282
1	NT_021877.18	396901	204945745	plus	G	ref_assembly	reference	reference	view	282

NCBI Resource Links

Submitter-Referenced
GenBank
NT_021877.12

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL591846.15 NC_000001.9	AL445652.6

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	N	T
ss23703558	AFD_EUR_PANEL	European	48	IG	0.125	0.625	0.250	0.200	0.438		0.562

	AFD_AFR_PANEL	African American	46	IG	0.304	0.435	0.261	0.584	0.522		0.478

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.292	0.583	0.200	0.271		0.729

ss5451882	HapMap-CEU	European	118	IG	0.305	0.424	0.271	0.251	0.517		0.483

	HapMap-HCB	Asian	90	IG	0.044	0.444	0.511	0.371	0.267		0.733

	HapMap-JPT	Asian	88	IG	0.182	0.500	0.318	1.000	0.432		0.568

	HapMap-YRI	Sub-Saharan African	120	IG	0.533	0.367	0.100	0.479	0.717		0.283

	CHMJ	Asian	74	IG					0.351	0.054	0.595

ss68790610	HapMap-CEU	European	120	GF	0.300	0.417	0.283		0.508		0.492

	HapMap-HCB	Asian	90	GF	0.044	0.467	0.489		0.278		0.722

	HapMap-JPT	Asian	90	GF	0.178	0.511	0.311		0.433		0.567

	HapMap-YRI	Sub-Saharan African	120	GF	0.533	0.367	0.100		0.717		0.283

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss23703558	71	13	32	26
ss5451882	269	78	125	64
ss68790610	269	78	126	65

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs4072677	332	90	150	91

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5189	ss5451882	T/T	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r23_ch1_HCB_perlegen:genotyping_1.0.0	1471340
5189	ss68790610	G/T	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr1-HapMap-HCB

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 .