Reference SNP(refSNP) Cluster Report: rs1059840

Reference SNP(refSNP) Cluster Report: rs1059840

refSNP ID: rs1059840
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_015956.2:c.*1T>A
NM_146387.1:c.*1T>A
NM_146388.1:c.*1076T>A
NT_011295.10:g.1633292T>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss90902227 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1059840 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
ss1542824	LEE\|835943	fwd/T	A/T	ggcccagcggccaccccgtaccactgttga	gtgaagcacctcttctgagccaggccgagc	09/13/00	10/10/03	86	cDNA	unknown
ss3251070	YUSUKE\|IMS-JST061155	fwd/T	A/T	ggcccagcggccaccccgtaccactgttga	gtgaagcacctcttctgagccaggccgagc	09/05/01	05/16/04	100	Genomic	unknown
ss4429272	LEE\|e835943	fwd/T	A/T	ggcccagcggccaccccgtaccactgttga	gtgaagcacctcttctgagccaggccgagc	04/26/02	10/10/03	106	cDNA	unknown
ss16253866	CGAP-GAI\|1507349	rev/B	A/T	gctcggcctggctcagaagaggtgcttcac	tcaacagtggtacggggtggccgctgggcc	11/18/03	11/22/03	120	cDNA	unknown
ss23642914	PERLEGEN\|afd4227183	fwd/T	A/T	ggcccagcggccaccccgtaccactgttga	gtgaagcacctcttctgagccaggccgagc	08/10/04	09/13/04	123	Genomic	unknown
ss66528382	AFFY\|SNP_A-4232754	fwd/T	A/T	cccgtaccactgttga	gtgaagcacctcttct	10/29/06	08/14/07	127	Genomic	unknown
ss76350854	AFFY\|AFFY_6_1M_SNP_A-4232754	fwd/	A/T	cccgtaccactgttga	gtgaagcacctcttct	08/28/07	08/30/07	129	Genomic	unknown
ss84731439	HGSV\|Cor19129_SNV_20070510.chr19_10231490	fwd/	A/T	ggcccagcggccaccccgtaccactgttga	gtgaagcacctcttctgagccaggccgagc	12/06/07	12/07/07	130	Genomic	unknown
ss90902227	BCMHGSC_JDW\|JWB-1143652	fwd/	A/T	ggcccagcggccaccccgtaccactgttga	gtgaagcacctcttctgagccaggccgagc	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 AGAGGCAGCC CCGGCCTGAC CGGCCCCCCG CCCCGCCCCC ACCCCGCCCC CAGGCCTAAA
 TGTGCACAGC ATGCTCAAGC ACCAGACGCT GGTCCTGACG CTGCCCACCG TCGCCTTCCT
 GGAGGACAAG CTGCTCTGGC AGGACTCACG TTACAGACCC CTCTACCCCT TCAGCCTGCC
 CTACAGCGAC TTCCCCCGAC CCCTACCCCA CGCTACCCAG GGCCCAGCGG CCACCCCGTA
 CCACTGTTGA
 W
 GTGAAGCACC TCTTCTGAGC CAGGCCGAGC CCCTGGCCGA CTTGGGAGCC TCAGGCCCAC
 GCCCACCCTT CGAGGAAGGT GTCACCTGGA CCCCTTCATT CCACGGAGGA AGCTGAGGCC
 ACAGGGAGCG GCCATCGCCA TTGGGAAGGG GCGACTCCAC GGAAAGCCCA GACGGGCTTC
 TGCATCCATT CCCTCTTTTT GTTTTTAAAA TAAATTGTAT TTTTGAATCA AGGAGGATAA
 AGATAACTTC

GeneView

GeneView via analysis of contig annotation: MRPL4 mitochondrial ribosomal protein L4

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_011295->NM_015956

function

reference

NT_011295->NM_146387

function

reference

NT_011295->NM_146388

function

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


reference	NT_011295->NM_015956->	1633292	forward		3' UTR

reference	NT_011295->NM_146387->	1633292	forward		3' UTR

reference	NT_011295->NM_146388->	1633292	forward	2158	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1059840 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838483.2	4324789	9950732	minus	A	alt_assembly_8	HuRef	HuRef	view	100
19	NT_011295.10	1633292	10231490	plus	T	ref_assembly	reference	reference	view	100
19	NW_927195.1	1482134	10265888	plus	T	alt_assembly_1	Celera	Celera	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
X07730 AI972032 Hs.171995

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank mRNA:
NM_015956.2 NM_146387.1 NM_146388.1	AB049635.1 AF132962.1 AY007152.1 BC009858.2

UniGene Cluster ID
279652

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss23642914	AFD_EUR_PANEL	European	44	IG	0.091	0.227	0.682	0.200	0.205	0.795

	AFD_AFR_PANEL	African American	44	IG		0.409	0.591	0.251	0.205	0.795

	AFD_CHN_PANEL	Asian	44	IG		0.227	0.773	0.584	0.114	0.886

	HapMap-CEU	European	120	IG	0.050	0.300	0.650	0.294	0.200	0.800

	HapMap-HCB	Asian	90	IG		0.156	0.844	0.584	0.078	0.922

	HapMap-JPT	Asian	88	IG		0.114	0.886	0.752	0.057	0.943

	HapMap-YRI	Sub-Saharan African	118	IG	0.017	0.237	0.746	1.000	0.136	0.864

ss3251070	CEPH		184	AF					0.030	0.970

ss66528382	HapMap-CEU	European	118	GF	0.051	0.305	0.644		0.203	0.797

	HapMap-HCB	Asian	90	GF		0.156	0.844		0.078	0.922

	HapMap-JPT	Asian	90	GF		0.111	0.889		0.056	0.944

	HapMap-YRI	Sub-Saharan African	120	GF	0.033	0.233	0.733		0.150	0.850

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.231+/-0.249	332	260	269	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

UNKNOWN

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Revised: May 25, 2006 1:38 PM .