Reference SNP(refSNP) Cluster Report: rs94872

Reference SNP(refSNP) Cluster Report: rs94872

refSNP ID: rs94872
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_005449.3:c.373+259A>G
NT_021877.18:g.604624T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss101369 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs94872 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
ss101369	TSC-CSHL\|TSC0132710	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	09/06/00	04/07/04	92	Genomic	95 %
ss376869	KWOK\|OVLP-000621-183374	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	06/30/00	10/10/03	79	Genomic	99 %
ss664234	SC_JCM\|AC068122.3_89786	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	07/27/00	10/10/03	85	Genomic	unknown
ss1180984	KWOK\|OVLP-000804-591384	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	09/02/00	10/10/03	87	Genomic	99 %
ss1181821	KWOK\|OVLP-000804-594223	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	09/02/00	10/10/03	87	Genomic	99 %
ss1686521	KWOK\|OVLP-000925-293953	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	10/05/00	10/10/03	87	Genomic	99 %
ss1687303	KWOK\|OVLP-000925-304651	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	10/05/00	10/10/03	87	Genomic	99 %
ss5460916	TSC-CSHL\|TSC0177257	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	09/21/02	10/10/03	108	Genomic	unknown
ss5907968	SC_JCM\|NT_021877.12_549952	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	01/10/03	10/10/03	111	Genomic	unknown
ss15422173	SC_SNP\|NT_021877.16_549952	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	11/14/03	11/22/03	120	Genomic	unknown
ss16420900	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_021877.16_549952	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	02/17/04	03/04/04	120	Genomic	unknown
ss17349591	CSHL-HAPMAP\|CSHL-HuCC-200402.chr1.NT_021877.16_549952	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	02/19/04	03/04/04	120	Genomic	unknown
ss20589952	SSAHASNP\|WGSA-200403-chr1.chr1.NT_021877.16_549952	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	03/18/04	03/18/04	121	Genomic	unknown
ss43937180	ABI\|hCV3152143	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	07/18/05	07/18/05	126	Genomic	unknown
ss66630328	ILLUMINA\|HumanHap300v1.1_rs94872	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	11/09/06	11/09/06	127	Genomic	unknown
ss67922281	ILLUMINA\|HumanHap550v1.1_rs94872	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	11/14/06	11/15/06	127	Genomic	unknown
ss68045705	ILLUMINA\|HumanHap650Yv1.0_rs94872	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	11/14/06	11/15/06	127	Genomic	unknown
ss71610356	ILLUMINA\|HumanHap650Yv3.0_rs94872	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	04/23/07	04/23/07	127	Genomic	unknown
ss75449045	ILLUMINA\|ILMN_Human_1M_rs94872	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	08/28/07	08/29/07	129	Genomic	unknown
ss79297710	ILLUMINA\|HumanHap300v2.0_rs94872	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	04/18/07	11/18/07	130	Genomic	unknown
ss83087739	HGSV\|Cor18555_SNV_20070510.chr1_203475240	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	11/27/07	12/04/07	130	Genomic	unknown
ss83362472	KRIBB_YJKIM\|KHS443726	fwd/T	A/G	tgttcatcctacccagggcatgaggggagt	gaggcttgagattgaggagaggctctgaga	12/04/07	12/04/07	130	Genomic	unknown
ss87948076	BCMHGSC_JDW\|JWB-0176503	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	02/26/08	02/27/08	129	Genomic	unknown
ss98263786	ILLUMINA\|HumanHap550v3.0__rs94872	rev/B	C/T	tctcagagcctctcctcaatctcaagcctc	actcccctcatgccctgggtaggatgaaca	04/20/07	03/31/08	130	Genomic	unknown

Fasta sequence (Legend)

 ACGTAAGTGA CAGCGGAGTC TATGCCTGCG GAGCGGGCAT GAACACAGAC CGGGGAAAGA
 CCCAGAAAGT CACCCTGAAT GTCCACAGTG GTAGGTTCCT CCGCTGATTG GAGGCTCAGA
 CTACCCAGAA AATGTTTCAC TTGGGAAGAT TGGAACAGCC ATCTAACTGT AACAGTCTCC
 TAGACTCTTA CACTGTTGCC ATATAAGCCA CATAATGATT GAGATCCATA TGAAACCTCA
 TAGTCAATTA CCTCCATGGT CCACACAATT TTCTACCCAA CATGTATGAA AAGAACAAGA
 TAGGTGCTCT CTTTGTATTG TTCATCCTAC CCAGGGCATG AGGGGAGT
 R
 GAGGCTTGAG ATTGAGGAGA GGCTCTGAGA TGGAGGAAAT TGGAAGCAAA AGGAAATAAC
 TATCCAACGT AATTGTCCCA TGAGAAATAA AGGAAAGACA CTAATTTATC CAGCCACATT
 TATAGGCCAA TCTTATTACT CTGTGACCTG ATCCTTTATT TCTCTGGAAC CCCGCCTTTC
 TCCTTTCCTC CACTGAGTTC CCCACACATA TGCAGCAGTA ATTCAACAGC CTAGAATCCC
 AATGACCTCT GCTGGTTTTG CAGGGAATGT TGACTGGACT AGGGGAACCA GTATTTCCTT
 CAAGGAAGCC CCCAACCCAG CTCCTTCTCT GCTTCTTTCA GTGGACCCTG CCCTCATCCC
 CTTACTGTCA TCCACTTTGG CTGAATAGCT TCAGTTTACA CCCAACCTCA TCTCCCCCTA
 GAGACACCAC ATATTTCTCT TTACTTCAAT AGATA

GeneView

GeneView via analysis of contig annotation: FAIM3 Fas apoptotic inhibitory molecule 3

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_021877->NM_005449

function

HuRef

NW_001838536->NM_005449

function

Celera

NW_926794->NM_005449

function

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


reference	NT_021877->NM_005449->NP_005440	604624	reverse	intron

HuRef	NW_001838536->NM_005449->NP_005440	517867	reverse	intron

Celera	NW_926794->NM_005449->NP_005440	504139	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs94872 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838536.1	517867	177785063	minus	T	alt_assembly_8	HuRef	HuRef	view	348
1	NW_926794.1	504139	180338379	minus	C	alt_assembly_1	Celera	Celera	view	348
1	NT_021877.18	604624	205153468	minus	T	ref_assembly	reference	reference	view	348

NCBI Resource Links

Submitter-Referenced
GenBank
NT_021877.12 AC068122.3 AL359089 AL359089.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC098935.2 NC_000001.9	AC023534.3 AC068122.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss101369	TSC_42_AA		84	AF					0.150	0.850

	TSC_42_C		84	AF					0.500	0.500

	TSC_42_A		84	AF					0.550	0.450

	CEPH		184	AF					0.540	0.460

	HapMap-CEU	European	120	IG	0.267	0.517	0.217	0.752	0.525	0.475

	HapMap-HCB	Asian	90	IG	0.467	0.378	0.156	0.273	0.656	0.344

	HapMap-JPT	Asian	90	IG	0.289	0.622	0.089	0.050	0.600	0.400

	HapMap-YRI	Sub-Saharan African	120	IG		0.083	0.917		0.042	0.958

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.490+/-0.068	270	210	0	0

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .