Reference SNP(refSNP) Cluster Report: rs6575433

Reference SNP(refSNP) Cluster Report: rs6575433

refSNP ID: rs6575433
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
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_001042518.1:c.393G>A
NM_175739.3:c.693G>A
NP_001035983.1:p.E131E
NP_783866.2:p.E231E
NT_026437.11:g.75933461C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10739892 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6575433 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
ss10739892	BCM_SSAHASNP\|chr14.NT_026437.10_74853750	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	06/30/03	10/25/06	116	Genomic	unknown
ss12287415	WI_SSAHASNP\|chr14.NT_026437.10_74853750	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	07/04/03	10/10/03	116	Genomic	unknown
ss16639210	CSHL-HAPMAP\|CSHL-HuAA-200402.chr14.NT_026437.10_74853750	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	02/17/04	03/04/04	120	Genomic	unknown
ss21186533	SSAHASNP\|WGSA-200403-chr14.chr14.NT_026437.10_74853750	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	03/19/04	03/19/04	121	Genomic	unknown
ss24602153	PERLEGEN\|afd0227612	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	08/10/04	09/13/04	123	Genomic	unknown
ss48408355	APPLERA_GI\|hCV2786235	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	09/28/05	11/03/06	126	Genomic	unknown
ss65728892	ILLUMINA\|Human1-rs6575433	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	10/10/06	10/10/06	127	Genomic	unknown
ss66846929	ILLUMINA\|HumanHap300v1.1_rs6575433	fwd/T	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	11/09/06	11/09/06	127	Genomic	unknown
ss67474493	ILLUMINA\|HumanHap550v1.1_rs6575433	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	11/14/06	11/14/06	127	Genomic	unknown
ss67830221	ILLUMINA\|HumanHap650Yv1.0_rs6575433	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	11/14/06	11/14/06	127	Genomic	unknown
ss69166973	PERLEGEN\|PGP00227612	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	01/30/07	03/31/08	127	Genomic	unknown
ss70874415	ILLUMINA\|HumanHap550v3.0__rs6575433	rev/T	A/G	cttttctctctttgtgctagccaagtggga	aagccctttcaccctgaatatacaagaaag	04/20/07	03/31/08	130	Genomic	unknown
ss71463876	ILLUMINA\|HumanHap650Yv3.0_rs6575433	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	04/23/07	04/23/07	127	Genomic	unknown
ss75872319	ILLUMINA\|ILMN_Human_1M_rs6575433	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	08/28/07	08/29/07	129	Genomic	unknown
ss79226660	ILLUMINA\|HumanHap300v2.0_rs6575433	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	04/18/07	11/18/07	130	Genomic	unknown
ss84507832	KRIBB_YJKIM\|KHS729262	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	12/04/07	12/07/07	130	Genomic	unknown
ss86348476	CANCER-GENOME\|15285	fwd/B	C/T	ctttcttgtatattcagggtgaaagggctt	tcccacttggctagcacaaagagagaaaag	01/25/08	01/25/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTCATCTTGC CCTTGCTAGG GAGGACAAAG AAGGCCACGG CATCTCCCTT GTAATCCATC
 TGCAGCACAA AGCAGTTCAG CTCTGTATCC ACCCCAAAAG CGAACTGCTC TTTCTGGTGC
 ATCATGGGGA CATGCACAGT GACCTGCTCG CCCACCAGGA ATGGGAAGTT CTTTCTTGTA
 TATTCAGGGT GAAAGGGCTT
 Y
 TCCCACTTGG CTAGCACAAA GAGAGAAAAG AAGTCTTTAT GTCAAAGTAC AATTAGTGAG
 GCAAAGACAG CAAACTgaaa tggggaatta cttctagtgg gtatgaggtt tctttttgag
 gtgacaaaaa aatgctctga tattacacag cggagtagtt gcccaaactt gtgaatatac
 taaaaagcaa taaaatggtg aattttatga catgtgaatt gtatttcaat taaAAATAGA
 ATTAGTTAAA TAGAACAACA TAAACTGAAG GTAACTTAGT AAGGGCTCAA ACCATACCAG
 TTTTCTTTCC TTCTCTTTCC TCTTTGCAgg atggatggat aaatgggtgg atagcctggc
 agatggaggg tggatggata gatgaatagc taatggataa atggttggct ggCtgggtgg
 atagatggat taatggatga atggatggat ggatgaaccg atagagggat agatagatga
 atagattagt ggataggtgg ttggctagct agatggctag ctaggtggat gaatggatgc
 atggatggat ggatggatgg atggatggat ggatagatgg atgaactgat ggatggaTAA
 ATGGGTGGAT AGTTTGCTGG ATGGGT

GeneView

GeneView via analysis of contig annotation: SERPINA9 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9

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_001042518

function

reference

NT_026437->NM_175739

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_026437->NM_001042518->NP_001035983	75933462	reverse	554	synonymous	A	Glu [E]	3	131
					contig reference	G	Glu [E]	3	131

reference	NT_026437->NM_175739->NP_783866	75933462	reverse	854	synonymous	A	Glu [E]	3	231
					contig reference	G	Glu [E]	3	231

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6575433 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	41744122	74989592	plus	T	alt_assembly_1	Celera	Celera	view	200
14	NW_001838113.2	794582	75113960	minus	A	alt_assembly_8	HuRef	HuRef	view	200
14	NT_026437.11	75933462	94003462	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_026437

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_001042518.1 NM_175739.3	AL132708.3 AL132990.4

3D structure mapping
NP_001035983 NP_783866

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10739892	HapMap-CEU	European	120	IG	0.217	0.433	0.350	0.343	0.433	0.567

	HapMap-HCB	Asian	90	IG	0.778	0.200	0.022	0.752	0.878	0.122

	HapMap-JPT	Asian	90	IG	0.622	0.356	0.022	0.479	0.800	0.200

	HapMap-YRI	Sub-Saharan African	120	IG	0.667	0.333		0.150	0.833	0.167

	CHMJ	Asian	74	IG					0.770	0.230

ss24602153	AFD_EUR_PANEL	European	44	IG	0.227	0.409	0.364	0.439	0.432	0.568

	AFD_AFR_PANEL	African American	46	IG	0.609	0.391		0.251	0.804	0.196

	AFD_CHN_PANEL	Asian	44	IG	0.818	0.182		0.655	0.909	0.091

ss48408355	AGI_ASP population	multiple	72	IG	0.444	0.444	0.111	1.000	0.667	0.333

ss69166973	HapMap-CEU	European	120	GF	0.217	0.433	0.350		0.433	0.567

	HapMap-HCB	Asian	90	GF	0.756	0.222	0.022		0.867	0.133

	HapMap-JPT	Asian	90	GF	0.600	0.378	0.022		0.789	0.211

	HapMap-YRI	Sub-Saharan African	120	GF	0.667	0.333			0.833	0.167

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss10739892	268	142	93	33
ss24602153	71	37	22	8
ss48408355	38	16	16	4
ss69166973	268	142	93	33

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs6575433	370	193	127	44

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5189	ss10739892	C/C	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0	5090000
5189	ss69166973	C/T	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr14-HapMap-HCB
5193	ss10739892	C/C	CSHL-HAPMAP	HapMap-JPT	NA18942	JA18942	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0	5090000
5193	ss69166973	C/T	CSHL-HAPMAP	HapMap-JPT	NA18942	JA18942	chr14-HapMap-JPT

Genotype data submitted for	379	samples from	370	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 .