Reference SNP(refSNP) Cluster Report: rs2389717

Reference SNP(refSNP) Cluster Report: rs2389717

refSNP ID: rs2389717
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002731.2:c.931-6621C>T
NM_182948.2:c.1072-6621C>T
NT_032977.8:g.54666161C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3351253 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2389717 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
ss3351253	TSC-CSHL\|TSC1592134	fwd/B	C/T	agcttttaaaatcttttcctcaaatgtatt	agtacccacatttaatctttatagaagacc	09/20/01	10/30/04	100	Genomic	unknown
ss24237981	PERLEGEN\|afd1062804	fwd/B	C/T	agcttttaaaatcttttcctcaaatgtatt	agtacccacatttaatctttatagaagacc	08/10/04	09/13/04	123	Genomic	unknown
ss44090822	ABI\|hCV26711552	fwd/B	C/T	agcttttaaaatcttttcctcaaatgtatt	agtacccacatttaatctttatagaagacc	07/18/05	07/18/05	126	Genomic	unknown
ss68772398	PERLEGEN\|PGP01062804	fwd/B	C/T	agcttttaaaatcttttcctcaaatgtatt	agtacccacatttaatctttatagaagacc	01/30/07	08/14/07	127	Genomic	unknown
ss75127999	ILLUMINA\|ILMN_Human_1M_rs2389717	fwd/B	C/T	agcttttaaaatcttttcctcaaatgtatt	agtacccacatttaatctttatagaagacc	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 CTGGGTAGTG CAAAACAGCA GTCCCCAAAG CAGGGCGTGC AAGGCAACCA GCTCTCAAAC
 AAAAAGATAA TATTAGAAGT CCCATTCCTA CTTATTTTTA CCTTATTCTT TTTCAATACC
 TTATTTGTGT GTGTATCTTA TAATAGTATA GTCATACATC TAAATAAATT GTAAGTAAAT
 AACTATATAT ATGTTGATTA TGTGTACTAG AAAATGTTTT AATGAAAGGG ATATAAATTA
 AAAACCCTTG GAGAGCTCTG GGCCAGAAGT GGAGAATCAT GAATATGAAA CCTGCTTTAG
 CCGCTTATCA GTCATGTGAA TTTGGTCAAT CGACTCTTTT ATAATCTGTA AAATGGGAGT
 AAGAACACCA GTCCTTCCTT CCTCACAGTG TTGTACTGAG AACAGAATAA AGCAACTGTA
 ATTGTTTGTA AATTCTATAA AGGCTGTGCA GATTATGATT TTTTTTTTTT AGCTTTTAAA
 ATCTTTTCCT CAAATGTATT
 Y
 AGTACCCACA TTTAATCTTT ATAGAAGACC ATATTCGAAG TAGTGGGAAG ACATTTTACT
 TTTAGGATCA AAGGAGAAAA ATGTTTAAGG TTTAACAATT CTCTAATTCT AAAAGAGTTA
 TATTTCTTTC CAAACTCTCA GAAAGTTTTG ATGGCCAGAT ATTTTAAACA AAATAAACTT
 GGGAATTAAA AAAGGAAAGC AATTAAAAGT AAGTCTGAGA TTTAGCTGTA ACTTGAGGAG
 AAAAGAATTT TT

GeneView

GeneView via analysis of contig annotation: PRKACB protein kinase, cAMP-dependent, catalytic, beta

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_032977->NM_002731

function

reference

NT_032977->NM_182948

function

HuRef

NW_001838589->NM_002731

function

HuRef

NW_001838589->NM_182948

function

Celera

NW_921795->NM_002731

function

Celera

NW_921795->NM_182948

function

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


reference	NT_032977->NM_002731->NP_002722	54666161	forward	intron

reference	NT_032977->NM_182948->NP_891993	54666161	forward	intron

HuRef	NW_001838589->NM_002731->NP_002722	19425464	reverse	intron

HuRef	NW_001838589->NM_182948->NP_891993	19425464	reverse	intron

Celera	NW_921795->NM_002731->NP_002722	745350	forward	intron

Celera	NW_921795->NM_182948->NP_891993	745350	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2389717 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_001838589.2	19425464	82804545	minus	G	alt_assembly_8	HuRef	HuRef	view	500
1	NW_921795.1	745350	82938456	plus	C	alt_assembly_1	Celera	Celera	view	500
1	NT_032977.8	54666161	84466830	plus	C	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000001.8

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL450063.14 NC_000001.9	AC027046.2 AC069041.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss24237981	AFD_EUR_PANEL	European	48	IG	0.583	0.375	0.042	1.000	0.771		0.229

	AFD_AFR_PANEL	African American	44	IG	0.682	0.273	0.045	0.752	0.818		0.182

	AFD_CHN_PANEL	Asian	48	IG	0.667	0.333		0.343	0.833		0.167

ss3351253	HapMap-CEU	European	118	IG	0.610	0.339	0.051	1.000	0.780		0.220

	HapMap-HCB	Asian	90	IG	0.556	0.400	0.044	0.584	0.756		0.244

	HapMap-JPT	Asian	88	IG	0.886	0.091	0.023	0.100	0.932		0.068

	HapMap-YRI	Sub-Saharan African	120	IG	0.883	0.100	0.017	0.150	0.933		0.067

	CHMJ	Asian	74	IG					0.851	0.027	0.122

ss68772398	HapMap-CEU	European	120	GF	0.617	0.333	0.050		0.783		0.217

	HapMap-HCB	Asian	90	GF	0.556	0.400	0.044		0.756		0.244

	HapMap-JPT	Asian	90	GF	0.889	0.089	0.022		0.933		0.067

	HapMap-YRI	Sub-Saharan African	120	GF	0.883	0.100	0.017		0.933		0.067

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24237981	71	45	23	2
ss3351253	269	195	65	7
ss68772398	269	197	65	7

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2389717	332	237	84	9

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
524	ss3351253	C/T	CSHL-HAPMAP	HapMap-CEU	NA12740	CEPH1444.02	r23_ch1_CEU_illumina:golden_gate_1.0.0	263805
524	ss68772398	C/C	CSHL-HAPMAP	HapMap-CEU	NA12740	CEPH1444.02	chr1-HapMap-CEU

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 .