Reference SNP(refSNP) Cluster Report: rs2749531

Reference SNP(refSNP) Cluster Report: rs2749531

refSNP ID: rs2749531
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_000295.3:c.-5+2205C>T
NM_001002235.1:c.-4-3114C>T
NM_001002236.1:c.-5+2205C>T
NT_026437.11:g.75852445G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3881937 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2749531 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
ss3881937	SC_JCM\|AL117259.5_4207	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	09/25/01	10/25/06	100	Genomic	unknown
ss24129863	PERLEGEN\|afd0227288	rev/T	A/G	tccctgcctaatctcacaccatttctaccc	ggagcataaaataagggaccaagagcaacc	08/10/04	09/13/04	123	Genomic	unknown
ss66808396	ILLUMINA\|HumanHap300v1.1_rs2749531	fwd/T	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	11/09/06	11/09/06	127	Genomic	unknown
ss67271491	ILLUMINA\|HumanHap550v1.1_rs2749531	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	11/14/06	11/14/06	127	Genomic	unknown
ss67672200	ILLUMINA\|HumanHap650Yv1.0_rs2749531	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	11/14/06	11/14/06	127	Genomic	unknown
ss69166933	PERLEGEN\|PGP00227288	rev/T	A/G	tccctgcctaatctcacaccatttctaccc	ggagcataaaataagggaccaagagcaacc	01/30/07	08/14/07	127	Genomic	unknown
ss70749957	ILLUMINA\|HumanHap550v3.0__rs2749531	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	04/20/07	03/30/08	130	Genomic	unknown
ss71322224	ILLUMINA\|HumanHap650Yv3.0_rs2749531	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	04/23/07	04/23/07	127	Genomic	unknown
ss75841829	ILLUMINA\|ILMN_Human_1M_rs2749531	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	08/28/07	08/29/07	129	Genomic	unknown
ss79145796	ILLUMINA\|HumanHap300v2.0_rs2749531	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	04/18/07	11/18/07	130	Genomic	unknown
ss84077404	KRIBB_YJKIM\|KHS629916	fwd/B	C/T	ggttgctcttggtcccttattttatgctcc	gggtagaaatggtgtgagattaggcaggga	12/04/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 ATTCTTTTCT CCATTGTACA GCTATGAAGC TAGTGCTCAA AGAAGTGAAG TCATTTACCC
 CAGGCCCCCT GCCAGTAAGT GACAGGGCCT GGTCACACTT GGGTTTATTT ATTGCCCAGT
 TCAACAGGTT GTTTGACCAT AGGCGAGATT CTCTTCCCTG CACCCTGCCG GGTTGCTCTT
 GGTCCCTTAT TTTATGCTCC
 Y
 GGGTAGAAAT GGTGTGAGAT TAGGCAGGGA GTGGCTCGCT TCCCTGTCCC TGGCCCCGCA
 AAGAGTGCTC CCACCTGCCC CGATCCCAGA AATGTCACCA TGAAGCCTTC ATTCTTTTGG
 TTTAAAGCTT GGCCTCAGTG TCCGTACACC ATGGGGTACT TGGCCAGATG GCGACTTTCT
 CCTCTCCAGT CGCCCTCCCA

GeneView

GeneView via analysis of contig annotation: SERPINA1 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1

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_000295

function

reference

NT_026437->NM_001002235

function

reference

NT_026437->NM_001002236

function

HuRef

NW_001838113->NM_000295

function

HuRef

NW_001838113->NM_001002235

function

HuRef

NW_001838113->NM_001002236

function

Celera

NW_925561->NM_000295

function

Celera

NW_925561->NM_001002235

function

Celera

NW_925561->NM_001002236

function

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


reference	NT_026437->NM_000295->NP_000286	75852445	reverse	intron

reference	NT_026437->NM_001002235->NP_001002235	75852445	reverse	intron

reference	NT_026437->NM_001002236->NP_001002236	75852445	reverse	intron

HuRef	NW_001838113->NM_000295->NP_000286	876280	forward	intron

HuRef	NW_001838113->NM_001002235->NP_001002235	876280	forward	intron

HuRef	NW_001838113->NM_001002236->NP_001002236	876280	forward	intron

Celera	NW_925561->NM_000295->NP_000286	41663125	reverse	intron

Celera	NW_925561->NM_001002235->NP_001002235	41663125	reverse	intron

Celera	NW_925561->NM_001002236->NP_001002236	41663125	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2749531 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	41663125	74908595	minus	G	alt_assembly_1	Celera	Celera	view	200
14	NW_001838113.2	876280	75032262	plus	C	alt_assembly_8	HuRef	HuRef	view	200
14	NT_026437.11	75852445	93922445	minus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000014.7 AL132708 K02212

dbSNP Blast Analysis
GenBank HTGS Finished:
AL117259.6 AL132708.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24129863	AFD_EUR_PANEL	European	48	IG	0.708	0.208	0.083	0.150	0.812	0.188

	AFD_AFR_PANEL	African American	42	IG	0.714	0.190	0.095	0.100	0.810	0.190

	AFD_CHN_PANEL	Asian	44	IG	0.091	0.227	0.682	0.200	0.205	0.795

ss3881937	HapMap-CEU	European	120	IG	0.567	0.400	0.033	0.371	0.767	0.233

	HapMap-HCB	Asian	90	IG	0.111	0.578	0.311	0.200	0.400	0.600

	HapMap-JPT	Asian	90	IG	0.178	0.511	0.311	1.000	0.433	0.567

	HapMap-YRI	Sub-Saharan African	120	IG	0.983	0.017		1.000	0.992	0.008

ss69166933	HapMap-CEU	European	120	GF	0.567	0.350	0.083		0.742	0.258

	HapMap-HCB	Asian	90	GF	0.111	0.200	0.689		0.211	0.789

	HapMap-JPT	Asian	90	GF	0.156	0.200	0.644		0.256	0.744

	HapMap-YRI	Sub-Saharan African	120	GF	0.983	0.017			0.992	0.008

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24129863	70
ss3881937	232	154	45	33
ss69166933	232

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2749531	332	154	45	33

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
200	ss3881937	C/T	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r23_ch14_CEU_illumina:infinium_genotyping_2.0.0
200	ss69166933	A/A	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	chr14-HapMap-CEU
255	ss3881937	C/C	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r23_ch14_CEU_illumina:infinium_genotyping_2.0.0
255	ss69166933	A/G	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	chr14-HapMap-CEU
349	ss3881937	C/T	CSHL-HAPMAP	HapMap-CEU	NA10861	CEPH1362.02	r23_ch14_CEU_illumina:infinium_genotyping_2.0.0
349	ss24129863	A/A	PERLEGEN	AFD_EUR_PANEL	NA10861		71_IND_CHR_14
349	ss69166933	A/A	CSHL-HAPMAP	HapMap-CEU	NA10861	CEPH1362.02	chr14-HapMap-CEU
535	ss3881937	C/T	CSHL-HAPMAP	HapMap-CEU	NA12750	CEPH1444.13	r23_ch14_CEU_illumina:infinium_genotyping_2.0.0
535	ss69166933	A/A	CSHL-HAPMAP	HapMap-CEU	NA12750	CEPH1444.13	chr14-HapMap-CEU
619	ss3881937	C/T	CSHL-HAPMAP	HapMap-CEU	NA12873	CEPH1459.10	r23_ch14_CEU_illumina:infinium_genotyping_2.0.0
619	ss69166933	A/A	CSHL-HAPMAP	HapMap-CEU	NA12873	CEPH1459.10	chr14-HapMap-CEU
5148	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5148	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	chr14-HapMap-HCB
5149	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18524	CH18524	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5149	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18524	CH18524	chr14-HapMap-HCB
5150	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5150	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	chr14-HapMap-HCB
5151	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5151	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	chr14-HapMap-HCB
5153	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5153	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	chr14-HapMap-HCB
5154	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18562	CH18562	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5154	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18562	CH18562	chr14-HapMap-HCB
5155	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18537	CH18537	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5155	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18537	CH18537	chr14-HapMap-HCB
5158	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18605	CH18605	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5158	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18605	CH18605	chr14-HapMap-HCB
5161	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5161	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	chr14-HapMap-HCB
5162	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5162	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	chr14-HapMap-HCB
5164	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5164	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	chr14-HapMap-HCB
5165	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5165	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	chr14-HapMap-HCB
5168	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18555	CH18555	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5168	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18555	CH18555	chr14-HapMap-HCB
5170	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5170	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	chr14-HapMap-HCB
5175	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18620	CH18620	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5175	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18620	CH18620	chr14-HapMap-HCB
5187	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5187	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	chr14-HapMap-HCB
5189	ss3881937	C/T	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r23_ch14_HCB_illumina:infinium_genotyping_2.0.0
5189	ss69166933	A/A	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr14-HapMap-HCB
5194	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18940	JA18940	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5194	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18940	JA18940	chr14-HapMap-JPT
5196	ss3881937	C/C	CSHL-HAPMAP	HapMap-JPT	NA18943	JA18943	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5196	ss69166933	A/G	CSHL-HAPMAP	HapMap-JPT	NA18943	JA18943	chr14-HapMap-JPT
5197	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18947	JA18947	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5197	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18947	JA18947	chr14-HapMap-JPT
5201	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5201	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	chr14-HapMap-JPT
5214	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18966	JA18966	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5214	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18966	JA18966	chr14-HapMap-JPT
5219	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18970	JA18970	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5219	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18970	JA18970	chr14-HapMap-JPT
5220	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5220	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	chr14-HapMap-JPT
5222	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5222	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	chr14-HapMap-JPT
5224	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5224	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	chr14-HapMap-JPT
5225	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5225	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	chr14-HapMap-JPT
5226	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18990	JA18990	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5226	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18990	JA18990	chr14-HapMap-JPT
5227	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5227	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	chr14-HapMap-JPT
5229	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5229	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr14-HapMap-JPT
5230	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA18997	JA18997	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5230	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA18997	JA18997	chr14-HapMap-JPT
5232	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA19000	JA19000	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5232	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA19000	JA19000	chr14-HapMap-JPT
5233	ss3881937	C/T	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	r23_ch14_JPT_illumina:infinium_genotyping_2.0.0
5233	ss69166933	A/A	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	chr14-HapMap-JPT

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

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .