Reference SNP(refSNP) Cluster Report: rs3775531

Reference SNP(refSNP) Cluster Report: rs3775531

refSNP ID: rs3775531
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001008925.1:c.53-188C>G
NM_001009922.1:c.631-188C>G
NM_015436.2:c.658-188C>G
NT_016354.18:g.955785G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44568797 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3775531 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
ss4961597	YUSUKE\|IMS-JST131121	fwd/T	C/G	gctcaaatctgccttttcattttctgaatt	agagccaccttaatagctttttagagtttt	08/07/02	10/10/03	107	Genomic	unknown
ss22146225	SSAHASNP\|WGSA-200403-chr4.chr4.NT_016354.16_902769	rev/B	C/G	aaaactctaaaaagctattaaggtggctct	aattcagaaaatgaaaaggcagatttgagc	03/20/04	03/21/04	121	Genomic	unknown
ss23903544	PERLEGEN\|afd3495965	rev/B	C/G	aaaactctaaaaagctattaaggtggctct	aattcagaaaatgaaaaggcagatttgagc	08/10/04	09/13/04	123	Genomic	unknown
ss44568797	ABI\|hCV1880356	rev/	C/G	aaaactctaaaaagctattaaggtggctct	aattcagaaaatgaaaaggcagatttgagc	07/19/05	11/03/06	126	Genomic	unknown
ss74833881	AFFY\|SNP_M-591239	fwd/T	C/G	gctcaaatctgccttttcattttctgaatt	agagccaccttaatagctttttagagtttt	08/09/07	08/09/07	128	Genomic	unknown
ss76759529	AFFY\|AFFY_6_1M_SNP_A-8621071	rev/	C/G	ctattaaggtggctct	aattcagaaaatgaaa	08/28/07	08/30/07	129	Genomic	unknown
ss92647694	BCMHGSC_JDW\|JWB-1803940	rev/	C/G	aaaactctaaaaagctattaaggtggctct	aattcagaaaatgaaaaggcagatttgagc	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 AACACTCTTT TTGGAATTTA ATTCATTCCT AAGGCAGAGA AGACAGGGAA CAGTATACTA
 AACCTAAAAA ATAAGCAAAA ATATTATTTG TGTAAAAATT TTGGTTTTAT TAATTGAGAT
 ACATTTCTGA CTGAAAAATA ATGAAATCAT GTTGTTATTT TGAATTATAA GTATCAGGTA
 TTCATCTGAT TATGCCTAGG TTAATTTTCT TGCTTGTACT ATTTATACTA TTTAATATTT
 GGAAACTATT TTAAAATAAG CTTTTTTTTT GCTCAAATCT GCCTTTTCAT TTTCTGAATT
 S
 AGAGCCACCT TAATAGCTTT TTAGAGTTTT CAGTGAAAAA ATAAGAAGAA ATTTCTACTT
 TTGGAAATTT TTAGACTTAT GTATGTATTT TCACATCTTT AATATGATTT TCAAGGGATT
 ATGAGTAGAC AATGCTACTT GTATTTATAA GGTTTAAAAT ACTTAATTTG AATTAATCTC
 TTTTCAGATT CTCTGCAATG ACTGTAATGG ACGATCCACT GTTCAGTTTC ATATATTAGG
 CATGAAATGT AAGATTTGTG AATCCTATAA TACTGCTCAA GCTGGAGGAC GTAGAATTTC

GeneView

GeneView via analysis of contig annotation: RCHY1 ring finger and CHY zinc finger domain containing 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_016354->NM_001008925

function

reference

NT_016354->NM_001009922

function

reference

NT_016354->NM_015436

function

HuRef

NW_001838915->NM_001008925

function

HuRef

NW_001838915->NM_001009922

function

HuRef

NW_001838915->NM_015436

function

Celera

NW_922162->NM_001008925

function

Celera

NW_922162->NM_001009922

function

Celera

NW_922162->NM_015436

function

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


reference	NT_016354->NM_001008925->NP_001008925	955785	reverse	intron

reference	NT_016354->NM_001009922->NP_001009922	955785	reverse	intron

reference	NT_016354->NM_015436->NP_056251	955785	reverse	intron

HuRef	NW_001838915->NM_001008925->NP_001008925	916135	reverse	intron

HuRef	NW_001838915->NM_001009922->NP_001009922	916135	reverse	intron

HuRef	NW_001838915->NM_015436->NP_056251	916135	reverse	intron

Celera	NW_922162->NM_001008925->NP_001008925	23529172	reverse	intron

Celera	NW_922162->NM_001009922->NP_001009922	23529172	reverse	intron

Celera	NW_922162->NM_015436->NP_056251	23529172	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3775531 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_001838915.1	916135	72154585	minus	C	alt_assembly_8	HuRef	HuRef	view	300
4	NW_922162.1	23529172	73704198	minus	G	alt_assembly_1	Celera	Celera	view	300
4	NT_016354.18	955785	76627088	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016354

dbSNP Blast Analysis
GenBank HTGS Finished:
AC096759.3 NC_000004.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss23903544	AFD_EUR_PANEL	European	42	IG	0.333	0.619	0.048	0.150	0.643	0.357

	AFD_AFR_PANEL	African American	32	IG	0.438	0.438	0.125	1.000	0.656	0.344

	AFD_CHN_PANEL	Asian	42	IG	0.286	0.429	0.286	0.527	0.500	0.500

ss44568797	HapMap-CEU	European	120	IG	0.450	0.433	0.117	1.000	0.667	0.333

	HapMap-HCB	Asian	90	IG	0.311	0.578	0.111	0.200	0.600	0.400

	HapMap-JPT	Asian	88	IG	0.523	0.295	0.182	0.050	0.670	0.330

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

ss4961597	JBIC-allele		1490	AF					0.655	0.345

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.469+/-0.120	332	260	9	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .