Reference SNP(refSNP) Cluster Report: rs336378

Reference SNP(refSNP) Cluster Report: rs336378

refSNP ID: rs336378
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:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_001101669.1:c.2642+1611T>C
NM_003866.2:c.2642+1611T>C
NT_016354.18:g.67549720A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss82828552 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs336378 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
ss429013	KWOK\|OVLP-000621-322352	fwd/B	C/T	tggtgatcttcttcttcttttggttttgtc	gtatatgaggaccgtgccagagtgtgagtg	06/30/00	10/10/03	79	Genomic	99 %
ss982937	KWOK\|OVLP-000804-590729	fwd/B	C/T	tggtgatcttcttcttcttttggttttgtc	gtatatgaggaccgtgccagagtgtgagtg	09/01/00	04/07/04	86	Genomic	99 %
ss1781362	KWOK\|OVLP-000925-374131	fwd/B	C/T	tggtgatcttcttcttcttttggttttgtc	gtatatgaggaccgtgccagagtgtgagtg	10/05/00	10/10/03	87	Genomic	99 %
ss3729082	SC_JCM\|AC025879.2_96403	fwd/B	C/T	tggtgatcttcttcttcttttggttttgtc	gtatatgaggaccgtgccagagtgtgagtg	09/25/01	10/10/03	100	Genomic	unknown
ss10181591	BCM_SSAHASNP\|chr4.NT_016606.15_4521238	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	06/27/03	10/25/06	116	Genomic	unknown
ss14630409	WI_SSAHASNP\|chr4.NT_016606.16_4549629	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	11/05/03	11/22/03	119	Genomic	unknown
ss22209100	SSAHASNP\|WGSA-200403-chr4.chr4.NT_016606.16_4549629	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	03/20/04	03/21/04	121	Genomic	unknown
ss23433902	PERLEGEN\|afd3598331	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	08/10/04	09/13/04	123	Genomic	unknown
ss66435793	AFFY\|SNP_A-2177693	rev/T	A/G	cacggtcctcatatac	gacaaaaccaaaagaa	10/29/06	08/14/07	127	Genomic	unknown
ss76212836	AFFY\|AFFY_6_1M_SNP_A-2177693	rev/T	A/G	cacggtcctcatatac	gacaaaaccaaaagaa	08/28/07	08/30/07	129	Genomic	unknown
ss82828552	HGSV\|Cor19240_SNV_20070510.chr4_143359178	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	11/30/07	12/03/07	130	Genomic	unknown
ss92808408	BCMHGSC_JDW\|JWB-1864534	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	02/26/08	03/03/08	129	Genomic	unknown
ss108412306	1000GENOMES\|CEU.trio.12.15.2008_1104503_chr4_143221023	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	12/15/08	12/15/08	130	Genomic	unknown
ss110719057	1000GENOMES\|NA19240_2008_12_16_995574_chr4_143221023	rev/T	A/G	cactcacactctggcacggtcctcatatac	gacaaaaccaaaagaagaagaagatcacca	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 TGTTATACTA TAGAACAATA TATTTTGGTA TTGCCTATGA TGGACATTAT ATATGCAATA
 CATTTGCTCA TGATATAGCA TTTGTGATGA TTCATTTTTG TGTTTTTAAG GTAAGGCACT
 AGAAATTTAA TCTAAAACAC TAAAGGCTTA ACTTCAAATC CCTAGTATTC TGGTGATCTT
 CTTCTTCTTT TGGTTTTGTC
 Y
 GTATATGAGG ACCGTGCCAG AGTGTGAGTG TTGGCCTGTA TTTGTGTGTA TGTATGCATG
 TATTTAAAGA AAATAAGATG AGTTCTTTTC TTTAATAACT GCCTTCATTT CCCTCTGGGT
 ATTTTGCCTT ACAATACAGG CTCATAGGTT TACAAGCTCT GGCAACACAG CAGAGTAGAT
 ATGAACATGA GGTTTGGGAG CCAGCTAATT TGAATCCAGG CTATATGCCA TACATTACCC
 ATAGGCAAGT TAGTCTCTCA CTGCCTCTTA GTGCCTTAGG GCAAGTTACT CAACCTCTTG
 TACCTCTCAG TTTCCTCATC TTTTAAAACA GACATGATAA TAGTAGCTCC ATTTTAGGAG
 TGTCTCGGGG ATTAAATGAA ATGATACATG TACAGGAATT AACAATGTTT GGCACATGGT
 AATCACTAAA TAATGTTGGT TAAAAAAATT AAAAAATCAA GGGCTGTAAT GTTAATACTC
 TGATTTTC

GeneView

GeneView via analysis of contig annotation: INPP4B inositol polyphosphate-4-phosphatase, type II, 105kDa

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_016354->NM_001101669

function

reference

NT_016354->NM_003866

function

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


reference	NT_016354->NM_001101669->NP_001095139	67549720	reverse	intron

reference	NT_016354->NM_003866->NP_003857	67549720	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs336378 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838921.1	3213003	138730764	minus	G	alt_assembly_8	HuRef	HuRef	view	200
4	NW_922217.1	22589842	140332363	minus	G	alt_assembly_1	Celera	Celera	view	200
4	NT_016354.18	67549720	143221023	minus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016606 AC044875 AC044875.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10181591	HapMap-CEU	European	120	IG	0.950	0.050		1.000	0.975	0.025

	HapMap-HCB	Asian	88	IG	0.864	0.114	0.023	0.150	0.920	0.080

	HapMap-JPT	Asian	88	IG	0.864	0.136		0.655	0.932	0.068

	HapMap-YRI	Sub-Saharan African	120	IG	0.283	0.500	0.217	1.000	0.533	0.467

ss23433902	AFD_EUR_PANEL	European	48	IG	0.958	0.042		1.000	0.979	0.021

	AFD_AFR_PANEL	African American	40	IG	0.350	0.550	0.100	0.439	0.625	0.375

	AFD_CHN_PANEL	Asian	46	IG	0.826	0.130	0.043	0.150	0.891	0.109

ss66435793	HapMap-CEU	European	118	GF	0.949	0.051			0.975	0.025

	HapMap-HCB	Asian	90	GF	0.867	0.111	0.022		0.922	0.078

	HapMap-JPT	Asian	90	GF	0.844	0.156			0.922	0.078

	HapMap-YRI	Sub-Saharan African	120	GF	0.283	0.500	0.217		0.533	0.467

ss982937	TSC_42_AA		84	AF					0.650	0.350

	TSC_42_C		84	AF					1.000

	TSC_42_A		84	AF					1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.284+/-0.248	332	260	269	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .