Reference SNP(refSNP) Cluster Report: rs1146574

Reference SNP(refSNP) Cluster Report: rs1146574

refSNP ID: rs1146574
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_000016.2:c.468+2115A>G
NT_032977.8:g.46174590A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1902075 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1146574 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
ss1902075	KWOK\|OVLP-000925-419351	fwd/B	C/T	catatccattagatagcaaattatgcagta	tgttacagcatgtaaaaagaaggaaggcat	10/06/00	10/25/06	87	Genomic	99 %
ss1902623	KWOK\|OVLP-000925-424959	fwd/B	C/T	catatccattagatagcaaattatgcagta	tgttacagcatgtaaaaagaaggaaggcat	10/06/00	10/10/03	87	Genomic	99 %
ss2185495	TSC-CSHL\|TSC0562643	fwd/B	C/T	catatccattagatagcaaattatgcagta	tgttacagcatgtaaaaagaaggaaggcat	10/19/00	10/10/03	92	Genomic	95 %
ss2625046	SC_JCM\|AL357314.6_12674	fwd/B	C/T	catatccattagatagcaaattatgcagta	tgttacagcatgtaaaaagaaggaaggcat	11/03/00	10/10/03	89	Genomic	unknown
ss11408783	WI_SSAHASNP\|chr1.NT_034383.4_1022849	rev/T	A/G	atgccttccttctttttacatgctgtaaca	tactgcataatttgctatctaatggatatg	07/03/03	10/10/03	116	Genomic	unknown
ss43840989	ABI\|hCV8367929	rev/T	A/G	atgccttccttctttttacatgctgtaaca	tactgcataatttgctatctaatggatatg	07/18/05	11/03/06	126	Genomic	unknown
ss87548201	BCMHGSC_JDW\|JWB-0068264	rev/T	A/G	atgccttccttctttttacatgctgtaaca	tactgcataatttgctatctaatggatatg	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 GTCTGTTTCA TAATACAGTG AAGTTTTTAG AGCCTGTGAA GTAAATGAGC CTGTTTTTTT
 CTATACAAAA TGGCTTGTCA CTACTGGTTC CTCAGAGTTG TTTTTGTCTT Cttttcttct
 ttttggtttc atatatatat atatatatat atatatatat atatatatat atatatattt
 gtgtgtgtgt gtggtggcag tctctcaacg ttgtccaggc tggtcttgaa ctcctggcct
 caagcgatcc tcctgccttg gcttcccaaa gtgttaagat tacaggcatg agccaccatg
 cctggccTGT TCTTGGCTTC TTATTTGATC ATTTTTATTT ATTTTTTTTC TGTATTATTT
 TTTACCATAA CATTATTTTC CAAAGTAAAA ACCCAAGGAG TTTAAACATT CAACAGTACA
 GAAAAGTGAA ACAATTTATA GCATATCCAT TAGATAGCAA ATTATGCAGT A
 Y
 TGTTACAGCA TGTAAAAAGA AGGAAGGCAT AAGAAAATGT TCATGTTGTT AAATAAAGAT
 GTACATAAAA CTACATGTAT ATAATGGGGG CTAACTGTTA AAAACACAAT TACATATTTA
 AAAATGTGGT AGGCACTACA ATAAGGAAGT AATACTAATT AACTCCATAT CTGAGGGATT
 ACAGATATTT TTGTTCTACT

GeneView

GeneView via analysis of contig annotation: ACADM acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain

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_032977->NM_000016

function

HuRef

NW_001838579->NM_000016

function

Celera

NW_921351->NM_000016

function

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


reference	NT_032977->NM_000016->NP_000007	46174590	forward	intron

HuRef	NW_001838579->NM_000016->NP_000007	7462111	reverse	intron

Celera	NW_921351->NM_000016->NP_000007	50303424	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1146574 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_001838579.2	7462111	74332611	plus	T	alt_assembly_8	HuRef	HuRef	view	471
1	NW_921351.1	50303424	74442566	minus	A	alt_assembly_1	Celera	Celera	view	471
1	NT_032977.8	46174590	75975259	minus	A	ref_assembly	reference	reference	view	471

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034383 AC026052 AL357314.6 AL359206 AL359206.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL357314.11	AL359206.3 AL592082.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1902075	HapMap-CEU	European	114	IG	0.123	0.421	0.456	0.752	0.333	0.667

	HapMap-HCB	Asian	90	IG		0.067	0.933	1.000	0.033	0.967

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.333	0.517	0.150	0.655	0.592	0.408

ss43840989	AoD_African_American		90	AF					0.590	0.410

	AoD_Caucasian		92	AF					0.300	0.700

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict	Additional Freq. Data
	0.396+/-0.203	270	210	0	0	ALFRED: The Allele Frequency Database

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 .