Reference SNP(refSNP) Cluster Report: rs1409433

Reference SNP(refSNP) Cluster Report: rs1409433

refSNP ID: rs1409433
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_001872.3:c.384+1075A>G
NM_016413.3:c.384+1075A>G
NT_024524.13:g.27635502T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss11071145 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1409433 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
ss2209960	TSC-CSHL\|TSC0599667	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	10/19/00	04/07/04	88	Genomic	95 %
ss5957036	SC_JCM\|NT_033922.2_4710477	rev/B	C/T	aacttatcacagcagtgacagtttcacctt	tatgaaggtgaaatcccacctatgaagcct	01/10/03	10/10/03	111	Genomic	unknown
ss11071145	BCM_SSAHASNP\|chr13.NT_024524.12_15229993	rev/B	C/T	aacttatcacagcagtgacagtttcacctt	tatgaaggtgaaatcccacctatgaagcct	07/01/03	04/07/04	116	Genomic	unknown
ss12241662	WI_SSAHASNP\|chr13.NT_024524.12_15229993	rev/B	C/T	aacttatcacagcagtgacagtttcacctt	tatgaaggtgaaatcccacctatgaagcct	07/04/03	10/10/03	116	Genomic	unknown
ss13284500	SC_SNP\|NT_024524.12_15229993	rev/B	C/T	aacttatcacagcagtgacagtttcacctt	tatgaaggtgaaatcccacctatgaagcct	10/22/03	10/31/03	119	Genomic	unknown
ss21148111	SSAHASNP\|WGSA-200403-chr13.chr13.NT_024524.13_27635502	rev/B	C/T	aacttatcacagcagtgacagtttcacctt	tatgaaggtgaaatcccacctatgaagcct	03/19/04	03/19/04	121	Genomic	unknown
ss28489581	PGA-UW-FHCRC\|CPB2-025645	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	08/16/04	09/13/04	126	Genomic	unknown
ss66671631	ILLUMINA\|HumanHap300v1.1_rs1409433	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	11/09/06	11/09/06	127	Genomic	unknown
ss67097875	ILLUMINA\|HumanHap550v1.1_rs1409433	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	11/14/06	11/14/06	127	Genomic	unknown
ss67432803	ILLUMINA\|HumanHap650Yv1.0_rs1409433	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	11/14/06	11/14/06	127	Genomic	unknown
ss70430290	ILLUMINA\|HumanHap300v2.0_rs1409433	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	04/18/07	11/18/07	127	Genomic	unknown
ss70614721	ILLUMINA\|HumanHap550v3.0__rs1409433	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	04/20/07	03/30/08	130	Genomic	unknown
ss71162590	ILLUMINA\|HumanHap650Yv3.0_rs1409433	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	04/23/07	04/23/07	127	Genomic	unknown
ss75594362	ILLUMINA\|ILMN_Human_1M_rs1409433	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	08/28/07	08/29/07	129	Genomic	unknown
ss82535027	HGSV\|Cor18956_SNV_20070510.chr13_45553502	rev/B	C/T	aacttatcacagcagtgacagtttcacctt	tatgaaggtgaaatcccacctatgaagcct	11/30/07	12/03/07	130	Genomic	unknown
ss83760314	KRIBB_YJKIM\|KHS536812	fwd/T	A/G	aggcttcataggtgggatttcaccttcata	aaggtgaaactgtcactgctgtgataagtt	12/04/07	12/05/07	130	Genomic	unknown
ss89646087	BCMHGSC_JDW\|JWB-0666589	rev/B	C/T	aacttatcacagcagtgacagtttcacctt	tatgaaggtgaaatcccacctatgaagcct	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCCCAGTTAA TTAAGCCAGA GTCAGTATGC TTCTAGAATG TGTGCCTGGT TGATTGAGGG
 GGCCTTAAAA TTGCACCCCC CCTTTTTTAA TCTCTCCTAC ATCTATCCAA CTTAGACCAC
 CTCTCTCCAG CATCCATCAG CACGACTGCA TGAGCAAACT TGATGCAGAG AGGCTTCATA
 GGTGGGATTT CACCTTCATA
 R
 AAGGTGAAAC TGTCACTGCT GTGATAAGTT TGGTGGGGAG AGGGGAATGC CATAAACAGA
 AGtattttta aatatttgtt aaaacatatt ttaattattt tGTTCAAAAA AGTTATGTTT
 TCTTACGATA TGTTCAGGAA AGAGTTGGAA TGACACAGGA GGAAAAAATA AGCACATGGC
 TCtattagtt ttctagggct gtggtaataa aataccacag actgtgtagc tgaaatcaca
 gaaatttgtt ttctcatgat tctagaggct agaagatcaa ggtgtcagta ggtttggttt
 ctactgaggc ctctttcctc agcttgtagg tagttgccat ctcacagcgt tcttcctcat
 atgccttttc tttccttttt tttttttttt ttttgagaca gagtttctct ctgtcaccca
 ggctggagtg cgatagcatg attttggctc actgcaacct gcgcctcttg ggttcaagca
 attctcctgc ctcagcctcc agagtagctg ggactagagg cgcataccac cacgctcagc
 taattttttg tatttttagt agagatggga tttcaccatg ttggacaggc tggtcttgaa
 ttcctgagct caagtgatct gctcgccttg gcctcccaaa attctaggat tacaggtgtg
 agccaccatg cccagcctca tatgaccttt tgtttgtgca catgcatccc tggtctctct
 ctgtatatct taatctcctc ttcatataag gacaccagtc agattggatt cgtgcccact
 ctaagggcct catgttgact tgatcatctc tttaaaggcc ctatctccaa atacagtcac
 tttctaacct actgggagtt agggattgaa catatgaatt ggagaaaggg gtacaacatc
 tactccttaa cTATGACATT ATAGAAAATG TCTTGTGCTT CTCTTTGCAC CCCCGCCCCT
 ATTATTTT

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

HuRef

NW_001838074->NM_001872

function

HuRef

NW_001838074->NM_016413

function

Celera

NW_925473->NM_001872

function

Celera

NW_925473->NM_016413

function

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


reference	NT_024524->NM_001872->NP_001863	27635502	reverse	intron

reference	NT_024524->NM_016413->NP_057497	27635502	reverse	intron

HuRef	NW_001838074->NM_001872->NP_001863	656312	reverse	intron

HuRef	NW_001838074->NM_016413->NP_057497	656312	reverse	intron

Celera	NW_925473->NM_001872->NP_001863	27445755	reverse	intron

Celera	NW_925473->NM_016413->NP_057497	27445755	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1409433 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	656312	27453303	minus	C	alt_assembly_8	HuRef	HuRef	view	200
13	NW_925473.1	27445755	27710531	minus	C	alt_assembly_1	Celera	Celera	view	200
13	NT_024524.13	27635502	45553502	minus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033922.2

dbSNP Blast Analysis
GenBank HTGS Finished:
AL137141.10 NC_000013.9

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss11071145	HapMap-CEU	European	120	IG	0.050	0.417	0.533	0.527	0.258	0.742

	HapMap-HCB	Asian	90	IG		0.289	0.711	0.273	0.144	0.856

	HapMap-JPT	Asian	88	IG	0.045	0.205	0.750	0.251	0.148	0.852

	HapMap-YRI	Sub-Saharan African	120	IG		0.117	0.883	0.655	0.058	0.942

ss2209960	SC_12_A	Asian	24	IG		0.250	0.750	0.655	0.125	0.875

	SC_12_AA	African American	20	IG	0.100	0.200	0.700	0.251	0.200	0.800

	SC_12_C	European	14	IG	0.143	0.571	0.286	0.752	0.429	0.571

ss28489581	PGA-AFRICAN-PANEL	African American	42	IG	0.048	0.190	0.762	0.317	0.143	0.857

	PGA-EUROPEAN-PANEL	European	38	IG	0.158	0.316	0.526	0.251	0.316	0.684

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss11071145	269
ss2209960	35	2	9	22
ss28489581	46	4	10	26

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1409433	335	6	17	45

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
229	ss2209960	A/G	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss11071145	C/C	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch13_CEU_illumina:golden_gate_1.0.0	808220

Genotype data submitted for	352	samples from	335	individuals	Individual with multiple genotypes submission:	17

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .