Reference SNP(refSNP) Cluster Report: rs2181617

Reference SNP(refSNP) Cluster Report: rs2181617

refSNP ID: rs2181617
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/129
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_001872.3:c.74+5754C>T
NM_016413.3:c.74+5754C>T
NT_024524.13:g.27653318G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss28489538 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2181617 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
ss3118616	TSC-CSHL\|TSC1225521	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	06/07/01	10/25/06	96	Genomic	unknown
ss5234962	TSC-CSHL\|TSC1226987	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	09/20/02	10/10/03	108	Genomic	unknown
ss13218150	SC_SNP\|NT_024524.12_15247809	rev/T	A/G	gctaaacgaattggagatgaaacatcataa	tgcaggtgcacaagtagaaaagtaaaatca	10/22/03	10/31/03	119	Genomic	unknown
ss21034962	SSAHASNP\|WGSA-200403-chr13.chr13.NT_024524.13_27653318	rev/T	A/G	gctaaacgaattggagatgaaacatcataa	tgcaggtgcacaagtagaaaagtaaaatca	03/19/04	03/19/04	121	Genomic	unknown
ss24666550	PERLEGEN\|afd0924371	rev/T	A/G	gctaaacgaattggagatgaaacatcataa	tgcaggtgcacaagtagaaaagtaaaatca	08/10/04	09/13/04	123	Genomic	unknown
ss28489538	PGA-UW-FHCRC\|CPB2-007826	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	08/16/04	09/13/04	126	Genomic	unknown
ss52086370	PGA-UW-FHCRC\|CPB2_007826	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	04/28/06	08/14/07	127	Genomic	unknown
ss66611687	ILLUMINA\|HumanHap300v1.1_rs2181617	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	11/09/06	11/09/06	127	Genomic	unknown
ss67231339	ILLUMINA\|HumanHap550v1.1_rs2181617	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	11/14/06	11/14/06	127	Genomic	unknown
ss67626893	ILLUMINA\|HumanHap650Yv1.0_rs2181617	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	11/14/06	11/14/06	127	Genomic	unknown
ss69133771	PERLEGEN\|PGP00924371	rev/T	A/G	gctaaacgaattggagatgaaacatcataa	tgcaggtgcacaagtagaaaagtaaaatca	01/30/07	08/14/07	127	Genomic	unknown
ss70709657	ILLUMINA\|HumanHap550v3.0__rs2181617	rev/T	A/G	gctaaacgaattggagatgaaacatcataa	tgcaggtgcacaagtagaaaagtaaaatca	04/20/07	03/30/08	130	Genomic	unknown
ss71276800	ILLUMINA\|HumanHap650Yv3.0_rs2181617	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	04/23/07	04/23/07	127	Genomic	unknown
ss75431525	ILLUMINA\|ILMN_Human_1M_rs2181617	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	08/28/07	08/29/07	129	Genomic	unknown
ss79118768	ILLUMINA\|HumanHap300v2.0_rs2181617	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	04/18/07	11/18/07	130	Genomic	unknown
ss83990373	KRIBB_YJKIM\|KHS594470	fwd/B	C/T	tgattttacttttctacttgtgcacctgca	ttatgatgtttcatctccaattcgtttagc	12/04/07	12/06/07	130	Genomic	unknown
ss89646157	BCMHGSC_JDW\|JWB-0666606	rev/T	A/G	gctaaacgaattggagatgaaacatcataa	tgcaggtgcacaagtagaaaagtaaaatca	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 TACTTTACAT GAAAAGGAAG CTTTGAGTTT GCCACATCTT TTGCTACAAC TCCCAAAATC
 ATGCCCAACC AACTTTTAAG TAAGGGCCAC AATCTTGACC CCAGCATTTA AGACCCTTAA
 CAATCAGGTC CTACCCTGCC ATTCGTCCTG GCTTTATTTC CTGGTATATC TCTATATAGG
 CCCCATATTT CTGCCCAGCT GGATCACTTC TCCTTCCTTG AGCTCTGATT TTACTTTTCT
 ACTTGTGCAC CTGCA
 Y
 TTATGATGTT TCATCTCCAA TTCGTTTAGC AAAATTCTGC CTATGTTAGT CTTATACCAT
 CTCATCTTCC CTTCACCTAT TGAATCCTAG TATCTCAGAA GTCCAACTCA GAATATCTCC
 ATTCTCTGAC TACCTAAGTC AAAAATGATA CCTGACTTTG TATTCCTGTA GCAGAATATT
 TATACCACTC GCATTGTACT TTTAGTGTTT TATCTCACAG AATAGGCATT TGTATCAGTT
 GCAGGTTAGT TTCCC

GeneView

GeneView via analysis of contig annotation: CPB2 carboxypeptidase B2 (plasma)

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_024524->NM_001872

function

reference

NT_024524->NM_016413

function

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


reference	NT_024524->NM_001872->NP_001863	27653318	reverse	intron

reference	NT_024524->NM_016413->NP_057497	27653318	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2181617 maps exactly once on NCBI human chromosome 13

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
13	NW_001838074.1	674128	27471119	minus	A	alt_assembly_8	HuRef	HuRef	view	255
13	NW_925473.1	27463570	27728346	minus	G	alt_assembly_1	Celera	Celera	view	255
13	NT_024524.13	27653318	45571318	minus	G	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024524

dbSNP Blast Analysis
GenBank HTGS Finished:
AL137141.10

UniGene Cluster ID
525011

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24666550	AFD_EUR_PANEL	European	48	IG	0.333	0.458	0.208	0.752	0.562	0.438

	AFD_AFR_PANEL	African American	46	IG	0.174	0.348	0.478	0.273	0.348	0.652

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.250	0.708	0.655	0.167	0.833

ss28489538	PGA-AFRICAN-PANEL	African American	46	IG	0.174	0.348	0.478	0.273	0.348	0.652

	PGA-EUROPEAN-PANEL	European	46	IG	0.348	0.478	0.174	1.000	0.587	0.413

	HapMap-CEU	European	118	IG	0.322	0.508	0.169	0.752	0.576	0.424

	HapMap-HCB	Asian	90	IG		0.356	0.644	0.150	0.178	0.822

	HapMap-JPT	Asian	88	IG	0.045	0.182	0.773	0.150	0.136	0.864

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.450	0.533	0.100	0.242	0.758

ss3118616	CHMJ	Asian	74	IG					0.108	0.892

ss52086370	HSP_GENO_PANEL		120	IG	0.117	0.433	0.450	1.000	0.333	0.667

	YRI_GENO_PANEL	Sub-Saharan African	120	IG	0.017	0.450	0.533	0.100	0.242	0.758

	AAM_GENO_PANEL	African American	124	IG	0.145	0.355	0.500	0.150	0.323	0.677

	CEU_GENO_PANEL	European	120	IG	0.317	0.517	0.167	0.752	0.575	0.425

	CHB_GENO_PANEL	Asian	90	IG		0.356	0.644	0.150	0.178	0.822

	JPT_GENO_PANEL	Asian	86	IG	0.023	0.186	0.791	0.584	0.116	0.884

ss69133771	HapMap-CEU	European	120	GF	0.317	0.517	0.167		0.575	0.425

	HapMap-HCB	Asian	90	GF		0.356	0.644		0.178	0.822

	HapMap-JPT	Asian	90	GF	0.044	0.200	0.756		0.144	0.856

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.450	0.533		0.242	0.758

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24666550	71
ss28489538	307	39	124	141
ss52086370	331	37	130	162
ss69133771	269

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2181617	455	55	173	200

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5225	ss28489538	T/T	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r23_ch13_JPT_illumina:golden_gate_1.0.0	809682
5225	ss52086370	T/T	PGA-UW-FHCRC	JPT_GENO_PANEL	NA18987	NA18987	CPB2-JPT-021307
5225	ss52086370	T/T	PGA-UW-FHCRC	JPT_GENO_PANEL	NA18987	NA18987	CPB2-JPT-040506
5225	ss69133771	A/G	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	chr13-HapMap-JPT

Genotype data submitted for	719	samples from	455	individuals	Individual with multiple genotypes submission:	307

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .