Reference SNP(refSNP) Cluster Report: rs1614348

Reference SNP(refSNP) Cluster Report: rs1614348

refSNP ID: rs1614348
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001002257.1:c.-5+6369G>A
NM_182551.3:c.-61-5800G>A
NT_022184.14:g.9492551G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16880565 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1614348 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
ss2429140	SC_JCM\|AC073255.3_12329	fwd/T	A/G	aggttttctttgatgaaaagtaaacatgac	gctatgaaactattatgaagaccgtagtag	11/03/00	10/10/03	89	Genomic	unknown
ss3801685	SC_JCM\|AC073255.4_147287	fwd/T	A/G	aggttttctttgatgaaaagtaaacatgac	gctatgaaactattatgaagaccgtaggta	09/25/01	10/10/03	100	Genomic	unknown
ss16880565	CSHL-HAPMAP\|CSHL-HuAA-200402.chr2.NT_022184.13_9492551	fwd/T	A/G	aggttttctttgatgaaaagtaaacatgac	gctatgaaactattatgaagaccgtaggta	02/17/04	10/26/06	120	Genomic	unknown
ss24156377	PERLEGEN\|afd1244062	fwd/T	A/G	aggttttctttgatgaaaagtaaacatgac	gctatgaaactattatgaagaccgtaggta	08/10/04	09/13/04	123	Genomic	unknown
ss44146116	ABI\|hCV2129586	fwd/T	A/G	aggttttctttgatgaaaagtaaacatgac	gctatgaaactattatgaagaccgtaggta	07/18/05	07/18/05	126	Genomic	unknown
ss66347957	AFFY\|SNP_A-1962530	fwd/T	A/G	gaaaagtaaacatgac	gctatgaaactattat	10/29/06	10/29/06	127	Genomic	unknown
ss76057275	AFFY\|AFFY_6_1M_SNP_A-1962530	fwd/T	A/G	gaaaagtaaacatgac	gctatgaaactattat	08/28/07	08/29/07	129	Genomic	unknown
ss80498521	HGSV\|Cor18507_SNV_20070510.chr2_30588269	fwd/T	A/G	aggttttctttgatgaaaagtaaacatgac	gctatgaaactattatgaagaccgtaggta	11/23/07	11/25/07	130	Genomic	unknown

Fasta sequence (Legend)

 CTGTTTGTGT AGCCTTTAAA TGAAAATTTA CCTGTGTAGA GTTAGGGAGG AAACTGATTG
 AAAGTTGGGG TGGCTTGAAC ACCAAAACGT TTCTTGACTA AACTCGATCA TTTTTGGATG
 TACACCATGA ACTTGGTGAT GGGGACAGAG TTAAATAAGA TGTGGTTTCT GTCTTTGAGC
 TTACTGTGTA GAGGGGGAGA TAAACACAAA TCAGTGCCTT CACTACAGAG GTCATTGAGA
 TTTCATCATC TGTAGGTTTT CTTTGATGAA AAGTAAACAT GAC
 R
 GCTATGAAAC TATTATGAAG ACCGTAGGTA GTAATGGTGA CCCTCTCTTT TAATAACGTG
 tgagtgccag gtgtatactg agttctgttc taagtgcttt aagtttttaa ctcctttaac
 cctcccagct tccactgtga agtaaataca aatactgtta ttatcctcat tttacttatg
 aggaaacaga agcccaaaga aggtacgggg catggatttg aacctacgca gtctagtttc
 agagtctgtg ctcttaatta ctatgctata atgCCTGTTT TAATGTACTG TAAATTTAAA
 ATATACTGTA CTTGTGTGGC ATTAAGTGTA AGGGATTATT TCAATGAGTA TGCCTTGTAT
 TACAAGTTAT GTCCAAAGTT TCTGAATATC CATGCTGAAT GTAACTTACG GTA

GeneView

GeneView via analysis of contig annotation: LYCAT lysocardiolipin acyltransferase 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_022184->NM_001002257

function

reference

NT_022184->NM_182551

function

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


reference	NT_022184->NM_001002257->NP_001002257	9492551	forward	intron

reference	NT_022184->NM_182551->NP_872357	9492551	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1614348 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838769.1	510868	30414624	plus	G	alt_assembly_8	HuRef	HuRef	view	283
2	NW_927719.1	30451637	30519702	plus	G	alt_assembly_1	Celera	Celera	view	283
2	NT_022184.14	9492551	30530122	plus	G	ref_assembly	reference	reference	view	283

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022184 AC015972

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G	N
ss16880565	HapMap-CEU	European	116	IG	0.069	0.397	0.534		0.267	0.733

	HapMap-HCB	Asian	90	IG	0.067	0.600	0.333		0.367	0.633

	HapMap-JPT	Asian	86	IG	0.093	0.326	0.581		0.256	0.744

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.433	0.533		0.250	0.750

	CHMJ	Asian	74	IG					0.297	0.662	0.041

ss24156377	AFD_EUR_PANEL	European	48	IG	0.083	0.333	0.583	0.655	0.250	0.750

	AFD_AFR_PANEL	African American	46	IG	0.087	0.304	0.609	0.439	0.239	0.761

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.583	0.333	0.251	0.375	0.625

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.406+/-0.195	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .