Reference SNP(refSNP) Cluster Report: rs11171

Reference SNP(refSNP) Cluster Report: rs11171

refSNP ID: rs11171
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/129
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_015908.4:c.2571C>T
NM_182800.2:c.2331C>T
NP_056992.4:p.D857D
NP_877952.1:p.D777D
NT_007933.14:g.25720385C>T
NT_007933.14:g.25720386C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48418341 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11171 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
ss13360	CGAP-GAI\|57002	fwd/T	A/G	caggtcccgatattccacaatggcccttgg	tctccacgaaccatcctgttgcgaggtttc	08/23/99	10/10/03	52	cDNA	99 %
ss1531256	LEE\|551310	rev/B	C/T	gaaacctcgcaacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	09/13/00	10/10/03	102	cDNA	unknown
ss1531326	LEE\|552601	rev/B	C/T	cctctcacctcacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	09/13/00	04/07/04	123	cDNA	unknown
ss4395927	LEE\|ge551310	rev/B	C/T	cctctcacctcacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	04/25/02	10/10/03	123	cDNA	unknown
ss4395960	LEE\|ge552601	rev/B	C/T	cctctcacctcacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	04/25/02	10/10/03	123	cDNA	unknown
ss4420513	LEE\|e551310	rev/B	C/T	gaaacctcgcaacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	04/26/02	10/10/03	108	cDNA	unknown
ss4420580	LEE\|e552601	rev/B	C/T	cctctcacctcacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	04/26/02	10/10/03	123	cDNA	unknown
ss16230856	CGAP-GAI\|1469851	fwd/T	A/G	caggtcccgatattccacaatggcccttgg	tctccacgaaccatcctgttgcgaggtttc	11/18/03	11/22/03	126	cDNA	unknown
ss23451769	PERLEGEN\|afd1580542	rev/B	C/T	cctctcacctcacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	08/10/04	09/13/04	123	Genomic	unknown
ss28526214	PGA-UW-FHCRC\|ACHE-009800	fwd/T	A/G	caggtcccgatattccacaatggcccttgg	tctccacgaaccatcctgtgaggtgagagg	11/05/04	01/27/05	126	Genomic	unknown
ss48418341	APPLERA_GI\|hCV8786528	fwd/T	A/G	caggtcccgatattccacaatggcccttgg	tctccacgaaccatcctgtgaagtgagagg	09/28/05	11/03/06	126	Genomic	unknown
ss68429106	CSHL-HAPMAP\|wicgr:assay:1123333:1	fwd/T	A/G	caggtcccgatattccacaatggcccttgg	tctccacgaaccatcctgtgaagtgagagg	01/11/07	01/16/07	127	NA	unknown
ss69023517	PERLEGEN\|PGP01580542	rev/B	C/T	cctctcacctcacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	01/30/07	08/14/07	127	Genomic	unknown
ss74815593	AFFY\|SNP_M-309871	fwd/T	A/G	caggtcccgatattccacaatggcccttgg	tctccacgaaccatcctgtgaggtgagagg	08/09/07	08/09/07	128	Genomic	unknown
ss75024894	ILLUMINA\|ILMN_Human_1M_rs11171	fwd/T	A/G	caggtcccgatattccacaatggcccttgg	tctccacgaaccatcctgtgaagtgagagg	08/28/07	08/29/07	129	Genomic	unknown
ss85394775	HGSV\|Cor19129_SNV_20070510.chr7_100130761	rev/B	C/T	cctctcacctcacaggatggttcgtggaga	ccaagggccattgtggaatatcgggacctg	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 TCCCACTGGT GTCCCTGCAA AGCCTGGCGC TTTTGACATC AATAATAAAA GTGGCAGGGC
 TGAGCAACAC CTCAGGAGTT ACTCTGGAAG GATGGAGGAG TTATGTAACA CACGAGAGTC
 AGGAGCCCTG TGGAAGTGCT TTTATTAGCA GTAAGGCTGA TCGTACAAAA AATTCTCAGA
 GCTTCATAGG ACAAGGTAGT ACAAGTATGG ATGATACAGG ACTGAGGAAC GGGGGACGGC
 TCAAAAGAAA TCAACATCGT CTGGGGCATC CAGGTCCCGA TATTCCACAA TGGCCCTTGG
 R
 TCTCCACGAA CCATCCTGTG AAGTGAGAGG TACAGGATGA GAGCTGAGGG CTCCCAAAAG
 GGAGTCTGCA GGCGGCAACA AAGCTTGGGC GTCTGCCCTC CTCACCTGTT GCGAGGTTTC
 CCAGGATAAC CTCCCTGGCC TCGGAAGGCA TCATAGTTCC CTCGACCAGC ACCATACGGG
 GCATGGGGGT ATGGAGGGCC TCCTGTGGGG ACTGCAGGGC GGACAGCACC AGCTATGACA
 GAGATCAGTG TTGAGTTGCA AAACTATGTC CTCAATTCCA TCCTCTGTTT TCTTCTCCCA

GeneView

GeneView via analysis of contig annotation: UFSP1 UFM1-specific peptidase 1 (non-functional)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: ACHE acetylcholinesterase (Yt blood group)

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_007933->NM_001015072

function

reference

NT_007933->NM_000665

function

reference

NT_007933->NM_015831

function

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


reference	NT_007933->NM_001015072->NP_001015072	25720386	reverse	3' near gene

reference	NT_007933->NM_000665->NP_000656	25720386	reverse	3' near gene

reference	NT_007933->NM_015831->NP_056646	25720386	reverse	3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11171 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839065.2	38756	95116488	plus	G	alt_assembly_8	HuRef	HuRef	view	300
7	NW_923574.1	23755728	95216691	minus	C	alt_assembly_1	Celera	Celera	view	300
7	NT_079595.2	25746927	99845715	minus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	300
7	NT_007933.14	25720386	100324046	minus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000007.8 AF082871 BG030779 Hs.111801

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_015908.4 NM_182800.2	AF002993.1	AK292467.1

UniGene Cluster ID
111801

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1531326	CEPH		184	AF					0.040	0.960

ss23451769	AFD_EUR_PANEL	European	48	IG	0.042		0.958	0.001	0.042	0.958

	AFD_AFR_PANEL	African American	44	IG	0.091	0.273	0.636	0.317	0.227	0.773

	AFD_CHN_PANEL	Asian	48	IG			1.000			1.000

ss28526214	PGA-AFRICAN-PANEL	African American	46	IG	0.087	0.348	0.565	0.655	0.261	0.739

	PGA-EUROPEAN-PANEL	European	46	IG	0.043		0.957	0.001	0.043	0.957

ss48418341	HapMap-CEU	European	120	IG		0.050	0.950	1.000	0.025	0.975

	HapMap-HCB	Asian	90	IG		0.022	0.978	1.000	0.011	0.989

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.433	0.483	1.000	0.300	0.700

	AGI_ASP population	multiple	40	IG	0.050	0.150	0.800	0.200	0.125	0.875

ss69023517	HapMap-CEU	European	120	GF		0.050	0.950		0.025	0.975

	HapMap-HCB	Asian	90	GF		0.022	0.978		0.011	0.989

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.083	0.433	0.483		0.300	0.700

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss23451769	70
ss28526214	46	3	7	35
ss48418341	291	9	46	234
ss69023517	270

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs11171	354	11	53	261

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
843	ss28526214	A/G	PGA-UW-FHCRC	PGA-AFRICAN-PANEL	D012		ACHE-AFRICAN-092304
843	ss23451769	C/C	PERLEGEN	AFD_AFR_PANEL	NA17112		71_IND_CHR_7

Genotype data submitted for	409	samples from	354	individuals	Individual with multiple genotypes submission:	307

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 .