Reference SNP(refSNP) Cluster Report: rs46725

Reference SNP(refSNP) Cluster Report: rs46725

refSNP ID: rs46725
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_001089.2:c.319+50G>A
NT_037887.4:g.2315962C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1462803 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs46725 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
ss413217	KWOK\|OVLP-000621-277674	fwd/T	A/G	tcggtgccaggcctagtggtgcctccacgc	gctgggcaggcaggggtcgagcccaggatg	06/30/00	10/10/03	79	Genomic	99 %
ss1238678	KWOK\|OVLP-000804-417860	fwd/T	A/G	tcggtgccaggcctagtggtgcctccacgc	gctgggcaggcaggggtcgagcccaggatg	09/02/00	10/10/03	87	Genomic	97 %
ss1462803	TSC-CSHL\|TSC0036674	fwd/T	A/G	tcggtgccaggcctagtggtgcctccacgc	gctgggcaggcaggggtcgagcccaggatg	09/07/00	10/25/06	92	Genomic	95 %
ss1646028	KWOK\|OVLP-000925-524982	fwd/T	A/G	tcggtgccaggcctagtggtgcctccacgc	gctgggcaggcaggggtcgagcccaggatg	10/04/00	10/10/03	87	Genomic	97 %
ss2515537	SC_JCM\|AC024088.4_129819	fwd/T	A/G	tcggtgccaggcctagtggtgcctccacgc	gctgggcaggcaggggtcgagcccaggatg	11/03/00	10/10/03	89	Genomic	unknown
ss10822543	BCM_SSAHASNP\|chr16.NT_037887.3_2315885	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	06/30/03	10/10/03	116	Genomic	unknown
ss12362753	WI_SSAHASNP\|chr16.NT_037887.3_2315885	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	07/04/03	10/10/03	116	Genomic	unknown
ss16720333	CSHL-HAPMAP\|CSHL-HuAA-200402.chr16.NT_037887.3_2315885	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	02/17/04	03/04/04	120	Genomic	unknown
ss21332168	SSAHASNP\|WGSA-200403-chr16.chr16.NT_037887.3_2315885	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	03/19/04	03/19/04	123	Genomic	unknown
ss43874575	ABI\|hCV971175	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	07/18/05	07/18/05	126	Genomic	unknown
ss70352131	PGA-UW-FHCRC\|ABCA3-015102	fwd/T	A/G	tcggtgccaggcctagtggtgcctccacgc	gctgggcaggcaggggtcgagcccaggatg	04/18/07	08/14/07	127	Genomic	unknown
ss78616846	HGSV\|Cor12878_SNV_20070510.chr16_2315962	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	10/17/07	10/20/07	129	Genomic	unknown
ss83901807	HGSV\|Cor18555_SNV_20070510.chr16_2315962	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	11/27/07	12/06/07	130	Genomic	unknown
ss90289170	BCMHGSC_JDW\|JWB-0908434	rev/B	C/T	catcctgggctcgacccctgcctgcccagc	gcgtggaggcaccactaggcctggcaccga	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCATCTGGCT CCGCTTGAAG ATTCAGTCGG AAAATGTGCC CAACGCCACC ATCTACCCGG
 GCCAGTCCAT CCAGGAGCTG CCTCTGTTCT TCACCTTCCC TCCGCCAGGA GACACCTGGG
 AGCTTGCCTA CATCCCTTCT CACAGTGACG CTGCCAAGAC CGTCACTGAG ACAGTGCGCA
 GGGCACTTGT GATCAACATG CGAGGTGAGA CATGCCGGGG CTCTCGGTGC CAGGCCTAGT
 GGTGCCTCCA CGC
 R
 GCTGGGCAGG CAGGGGTCGA GCCCAGGATG TGCGAAGCAG CTGGGTGAGG AGTTCACCCT
 GTGCAGACTT GGCCTCTGCT TCTTCCCGCA TCACTACTTC AACCTGTAAA AGGCACTGCT
 GTTCCTTAAA CCTCTGCCTG CCTGCGAGTA AATAGCAGTC TCTCCTTTGG GTCCGATAGC
 ACCATCACAG TCCCCACCAA AGGGACCCTG GTGACATTTT AACCCATGGG GCAGAACAGG
 TTAGAAAATG CACCTGCCTG CAGTTGCCCC AGGCTCCTTT CTGGTCCCTC ATTTTATGAA
 AGACATTACT GGTCTCCAGG CCTCTGTGAA CAGAGTCCAA ATAGATACAT AAGGAAAGTA
 GCAGATATTT GGGACTTAAA TACGACCTTG CCAGAAAAGG GAAAAAAGAA GGGAGGTTTT
 TGCTTGCCTG ATGGCACTAA GACTAGGGAG CCATCAAGC

GeneView

GeneView via analysis of contig annotation: ABCA3 ATP-binding cassette, sub-family A (ABC1), member 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_037887->NM_001089

function

HuRef

NW_001838339->NM_001089

function

Celera

NW_926018->NM_001089

function

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


reference	NT_037887->NM_001089->NP_001080	2315962	reverse	intron

HuRef	NW_001838339->NM_001089->NP_001080	322218	forward	intron

Celera	NW_926018->NM_001089->NP_001080	2306045	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs46725 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838339.2	322218	2301799	plus	A	alt_assembly_8	HuRef	HuRef	view	253
16	NT_037887.4	2315962	2315962	minus	C	ref_assembly	reference	reference	view	253
16	NW_926018.1	2306045	2590395	minus	T	alt_assembly_1	Celera	Celera	view	253

NCBI Resource Links

Submitter-Referenced
GenBank
NT_037887 AC005212 AC024088.4

dbSNP Blast Analysis
GenBank HTGS Finished:
AC005212.1 AC098805.2 NC_000016.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1462803	HapMap-CEU	European	120	IG	1.000				1.000

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	88	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.133	0.600	0.267	0.100	0.433	0.567

ss70352131	PGA_CEPH-PANEL	European	46	AF	1.000				1.000

	PGA_YORUB-PANEL	Sub-Saharan African	48	AF	0.125	0.667	0.208		0.458	0.542

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.300+/-0.245	270	210	47	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

YES

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Revised: May 25, 2006 1:38 PM .