Reference SNP(refSNP) Cluster Report: rs2854946

Reference SNP(refSNP) Cluster Report: rs2854946

refSNP ID: rs2854946
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/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_000624.3:c.-18+332C>G
NT_026437.11:g.76048132C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10725062 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2854946 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
ss4041968	SC_JCM\|M68516.1_2629	fwd/B	C/G	tctgttgttttctgtgcctggagtcttggg	ctttagaaatcaggaacaatgatccaatat	09/26/01	10/10/03	100	Genomic	unknown
ss10725062	BCM_SSAHASNP\|chr14.NT_026437.10_74968420	fwd/B	C/G	tctgttgttttctgtgcctggagtcttggg	ctttagaaatcaggaacaatgatccaatat	06/30/03	04/07/04	116	Genomic	unknown
ss12273141	WI_SSAHASNP\|chr14.NT_026437.10_74968420	fwd/B	C/G	tctgttgttttctgtgcctggagtcttggg	ctttagaaatcaggaacaatgatccaatat	07/04/03	10/10/03	116	Genomic	unknown
ss16648902	CSHL-HAPMAP\|CSHL-HuAA-200402.chr14.NT_026437.10_74968420	fwd/B	C/G	tctgttgttttctgtgcctggagtcttggg	ctttagaaatcaggaacaatgatccaatat	02/17/04	03/04/04	120	Genomic	unknown
ss23648676	PERLEGEN\|afd0228175	fwd/B	C/G	tctgttgttttctgtgcctggagtcttggg	ctttagaaatcaggaacaatgatccaatat	08/10/04	09/13/04	123	Genomic	unknown
ss65937667	AFFY\|SNP_A-1699743	rev/T	C/G	ggatcattgttcctgatttctaaag	cccaagactccaggcacagaaaaca	10/26/06	10/26/06	127	Genomic	unknown
ss66189483	AFFY\|SNP_A-2248662	rev/T	C/G	ttcctgatttctaaag	cccaagactccaggca	10/27/06	08/14/07	127	Genomic	unknown
ss76263778	AFFY\|AFFY_6_1M_SNP_A-2248662	rev/	C/G	ttcctgatttctaaag	cccaagactccaggca	08/28/07	08/30/07	130	Genomic	unknown
ss77181160	HGSV\|Cor12156_SNV_20070510.chr14_94118132	fwd/	C/G	tctgttgttttctgtgcctggagtcttggg	ctttagaaatcaggaacaatgatccaatat	10/09/07	10/11/07	129	Genomic	unknown
ss78079486	HGSV\|Cor12878_SNV_20070510.chr14_94118132	fwd/	C/G	tctgttgttttctgtgcctggagtcttggg	ctttagaaatcaggaacaatgatccaatat	10/17/07	10/17/07	129	Genomic	unknown

Fasta sequence (Legend)

 TTTTGGGGTT TGGGGTCTGC AAAGCTCTGA AGGAGTCTCA TCTCTGCAGT TTCAGGTATC
 CAAGGCAGCA GAGGTGAGTG GGTCCCCCGa gctctgtgac cttatgctcc acactaactc
 tggcagagcc tccgtttcct cataggtaag atggaaataa ttacaccctc tggatggtgt
 gactgaagat taaatACAGC GGGTGCTCTC ACTCAGCaca tctggccatg tctgcagaca
 catttggttg ccacaactgg aaggggggtg ggggttagtg acatctagag gccagcgatg
 ctgctgatga tcccacaatg cccaggacaa gatcacaaag catcatcctg ttcaaaaggt
 caacaggatc aaggttgaga gaccctgAAA TAAGGCCATG GGGACAAAAT GTCGGCTGGA
 TAGGAGGTGC TCAGTAAGTG GCAGCTTCTG TTGTTTTCTG TGCCTGGAGT CTTGGG
 S
 CTTTAGAAAT CAGGAACAAT GATCCAATAT TATCGGCTTC CGTGAGATAA GGGCATCTTG
 CCTGGAGGCT GCCACCCAGG CCGGTCATGG CAGCTGCTCA TGAAGGACAG TAACAATTTG
 GCAGTTTGTT AAATGAACAA AATGTAGAAA TAAAGTAAGC AGAATTTTTA GTTTTTCTGA
 AGGTAGGGCT TTTGGCCAGA

GeneView

GeneView via analysis of contig annotation: SERPINA5 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5

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_026437->NM_000624

function

HuRef

NW_001838113->NM_000624

function

Celera

NW_925561->NM_000624

function

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


reference	NT_026437->NM_000624->NP_000615	76048132	forward	intron

HuRef	NW_001838113->NM_000624->NP_000615	679736	reverse	intron

Celera	NW_925561->NM_000624->NP_000615	41859081	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2854946 maps exactly once on NCBI human chromosome 14

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
14	NW_925561.1	41859081	75104551	plus	C	alt_assembly_1	Celera	Celera	view	476
14	NW_001838113.2	679736	75228806	minus	G	alt_assembly_8	HuRef	HuRef	view	476
14	NT_026437.11	76048132	94118132	plus	C	ref_assembly	reference	reference	view	476

NCBI Resource Links

Submitter-Referenced
GenBank
NT_026437 AL049839 AL132990

dbSNP Blast Analysis
GenBank HTGS Finished:
AL049839.3 AL132990.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss10725062	AfAm	African American	12	IG	0.500	0.333	0.167	0.584	0.667	0.333

	Caucasian	European	20	IG	0.600	0.400		0.439	0.800	0.200

	Asian	Asian	12	IG	1.000				1.000

	CEPH	European	12	IG	0.833	0.167		1.000	0.917	0.083

	PDpanel	Global	38	IG	0.526	0.421	0.053	0.752	0.737	0.263

	HapMap-CEU	European	120	IG	0.683	0.317		0.200	0.842	0.158

	HapMap-HCB	Asian	90	IG	0.756	0.244		1.000	0.878	0.122

	HapMap-JPT	Asian	90	IG	0.889	0.111		1.000	0.944	0.056

	HapMap-YRI	Sub-Saharan African	120	IG	0.500	0.400	0.100		0.700	0.300

ss23648676	AFD_EUR_PANEL	European	48	IG	0.708	0.292		0.439	0.854	0.146

	AFD_AFR_PANEL	African American	46	IG	0.609	0.391		0.251	0.804	0.196

	AFD_CHN_PANEL	Asian	48	IG	0.833	0.167		0.752	0.917	0.083

ss66189483	HapMap-CEU	European	118	GF	0.678	0.322			0.839	0.161

	HapMap-HCB	Asian	90	GF	0.756	0.244			0.878	0.122

	HapMap-JPT	Asian	90	GF	0.889	0.111			0.944	0.056

	HapMap-YRI	Sub-Saharan African	120	GF	0.500	0.400	0.100		0.700	0.300

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.280+/-0.248	373	300	275	0

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .