Reference SNP(refSNP) Cluster Report: rs2071699

Reference SNP(refSNP) Cluster Report: rs2071699

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/130
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
NG_007510.1:g.9144C>T
NM_000148.2:c.35C>T
NM_000148.3:c.35C>T
NP_000139.1:p.Ala12Val
NT_011109.15:g.21522694G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss35073236 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2071699 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
ss2985392	YUSUKE\|IMS-JST007271	fwd/B	C/T	ggctccggagccatcgtcagctctgcctgg	cttcctgctagtctgtgtcctctctgtaat	05/24/01	10/10/03	96	Genomic	unknown
ss3186721	HGBASE\|SNP000572305	fwd/B	C/T	cggagccatcgtcagctctgcctgg	cttcctgctagtctgtgtcctctct	07/09/01	10/10/03	98	Genomic	unknown
ss24074059	PERLEGEN\|afd4231042	rev/T	A/G	attacagagaggacacagactagcaggaag	ccaggcagagctgacgatggctccggagcc	08/10/04	09/13/04	123	Genomic	unknown
ss35073236	PGA-UW-FHCRC\|FUT1-003343	fwd/B	C/T	ggctccggagccatcgtcagctctgcctgg	cttcctgctagtctgtgtcctctctgtaat	03/02/05	11/02/06	125	Genomic	unknown
ss69229834	PERLEGEN\|PGP04231042	rev/T	A/G	attacagagaggacacagactagcaggaag	ccaggcagagctgacgatggctccggagcc	01/30/07	08/14/07	127	Genomic	unknown
ss74807672	AFFY\|SNP_M-178451	fwd/B	C/T	ggctccggagccatcgtcagctctgcctgg	cttcctgctagtctgtgtcctctctgtaat	08/09/07	08/09/07	128	Genomic	unknown
ss74872175	ILLUMINA\|ILMN_Human_1M_rs2071699	fwd/B	C/T	ggctccggagccatcgtcagctctgcctgg	cttcctgctagtctgtgtcctctctgtaat	08/28/07	08/29/07	129	Genomic	unknown
ss76522213	AFFY\|AFFY_6_1M_SNP_A-8383371	rev/T	A/G	acagactagcaggaag	ccaggcagagctgacg	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 TCTTCCAGTC CCCATGCCCC GAAATTCCAA GGCTCTCATC CCTGAAACCT AGGACTCAGG
 CTCTCCCTAC CTCAGCCCCA GGAGTCTAAA CCTTTAACTT CCTCTTTCCC TGGGACTAAG
 GAGTGCTGCA CCCCAGGCGC CTCCCTTACC CCACATCCCT CCTCAGCCTC CCCTCCTCAG
 CCTCAGTGCA TTTGCTAATT CGCCTTTCCT CCCCTGCAGC CATGTGGCTC CGGAGCCATC
 GTCAGCTCTG CCTGG
 Y
 CTTCCTGCTA GTCTGTGTCC TCTCTGTAAT CTTCTTCCTC CATATCCATC AAGACAGCTT
 TCCACATGGC CTAGGCCTGT CGATCCTGTG TCCAGACCGC CGCCTGGTGA CACCCCCAGT
 GGCCATCTTC TGCCTGCCGG GTACTGCGAT GGGCCCCAAC GCCTCCTCTT CCTGTCCCCA
 GCACCCTGCT TCCCTCTCCG GCACCTGGAC TGTCTACCCC AATGGCCGGT TTGGTAATCA
 GATGGGACAG TATGC

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
Z69587.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24074059	AFD_EUR_PANEL	European	46	IG	0.870	0.130		0.752	0.935	0.065

	AFD_AFR_PANEL	African American	46	IG	1.000				1.000

	AFD_CHN_PANEL	Asian	48	IG	0.583	0.417		0.200	0.792	0.208

ss35073236	HapMap-CEU	European	120	IG	0.983	0.017		1.000	0.992	0.008

	HapMap-HCB	Asian	90	IG	0.600	0.333	0.067	0.655	0.767	0.233

	HapMap-JPT	Asian	88	IG	0.364	0.591	0.045	0.050	0.659	0.341

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

	PGA_CEPH-PANEL	European	34	IG	0.941	0.059		1.000	0.971	0.029

	PGA_YORUB-PANEL	Sub-Saharan African	46	IG	1.000				1.000

ss69229834	HapMap-CEU	European	120	GF	0.900	0.100			0.950	0.050

	HapMap-HCB	Asian	90	GF	0.600	0.356	0.044		0.778	0.222

	HapMap-JPT	Asian	88	GF	0.295	0.636	0.068		0.614	0.386

	HapMap-YRI	Sub-Saharan African	120	GF	0.817	0.183			0.908	0.092

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24074059	71
ss35073236	839	547	159	26

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2071699	919	547	159	26

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
169	ss35073236	C/C	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	r27_ch19_CEU_illumina:human_1m_beadchip
171	ss35073236	C/C	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	r27_ch19_CEU_illumina:human_1m_beadchip
225	ss35073236	C/C	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch19_CEU_illumina:human_1m_beadchip
226	ss35073236	C/C	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch19_CEU_illumina:human_1m_beadchip
255	ss35073236	C/T	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r27_ch19_CEU_illumina:human_1m_beadchip
429	ss35073236	C/C	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r27_ch19_CEU_illumina:human_1m_beadchip
621	ss35073236	C/C	CSHL-HAPMAP	HapMap-CEU	NA12875	CEPH1459.12	r27_ch19_CEU_illumina:human_1m_beadchip
5135	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	r27_ch19_YRI_bcm:genotype_0002
5142	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r27_ch19_YRI_bcm:genotype_0002
5144	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r27_ch19_YRI_bcm:genotype_0002
5170	ss35073236	T/T	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	r27_ch19_CHB_illumina:human_1m_beadchip
5211	ss35073236	C/C	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	r27_ch19_JPT_illumina:human_1m_beadchip
5213	ss35073236	C/T	CSHL-HAPMAP	HapMap-JPT	NA18973	JA18973	r27_ch19_JPT_illumina:human_1m_beadchip
5215	ss35073236	C/C	CSHL-HAPMAP	HapMap-JPT	NA18975	JA18975	r27_ch19_JPT_illumina:human_1m_beadchip
5225	ss35073236	C/C	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r27_ch19_JPT_illumina:human_1m_beadchip
5233	ss35073236	C/T	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	r27_ch19_JPT_illumina:human_1m_beadchip
5249	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA18516	YOR013.03	r27_ch19_YRI_bcm:genotype_0002
5256	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	r27_ch19_YRI_bcm:genotype_0002
5259	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r27_ch19_YRI_bcm:genotype_0002
5260	ss35073236	C/C	PGA-UW-FHCRC	PGA_YORUB-PANEL	DY12	NA18855	FUT1-PGA_YORUB-022505
5260	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r27_ch19_YRI_bcm:genotype_0002
5264	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	r27_ch19_YRI_bcm:genotype_0002
5265	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	r27_ch19_YRI_bcm:genotype_0002
5267	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r27_ch19_YRI_bcm:genotype_0002
5274	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	r27_ch19_YRI_bcm:genotype_0002
5275	ss35073236	C/C	PGA-UW-FHCRC	PGA_YORUB-PANEL	DY07	NA19137	FUT1-PGA_YORUB-022505
5275	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r27_ch19_YRI_bcm:genotype_0002
5276	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	r27_ch19_YRI_bcm:genotype_0002
5289	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19208	YOR051.01	r27_ch19_YRI_bcm:genotype_0002
5294	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r27_ch19_YRI_bcm:genotype_0002
5302	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19140	YOR071.02	r27_ch19_YRI_bcm:genotype_0002
5307	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r27_ch19_YRI_bcm:genotype_0002
5310	ss35073236	C/C	CSHL-HAPMAP	HapMap-YRI	NA19129	YOR077.01	r27_ch19_YRI_bcm:genotype_0002

Genotype data submitted for	981	samples from	919	individuals	Individual with multiple genotypes submission:	62

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .