Variant report

Variant	rs4889067
Chromosome Location	chr16:80058041-80058042
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:80052898..80058811-chr16:80059069..80065197,11	MCF-7	breast:
2	chr16:79802080..79804842-chr16:80056465..80059230,3	MCF-7	breast:
3	chr16:80057651..80058466-chr16:80118533..80119366,4	MCF-7	breast:
4	chr16:80057651..80058518-chr16:80118488..80119366,5	MCF-7	breast:
5	chr16:80045568..80049024-chr16:80056361..80060062,5	MCF-7	breast:
6	chr16:79071263..79072123-chr16:80057638..80058489,4	MCF-7	breast:
7	chr16:80051534..80054466-chr16:80056610..80058867,2	MCF-7	breast:
8	chr16:80032529..80034163-chr16:80057052..80059822,2	MCF-7	breast:
9	chr16:80056858..80058802-chr16:80070010..80071819,2	MCF-7	breast:
10	chr16:79640662..79643059-chr16:80057931..80060430,2	MCF-7	breast:
11	chr16:80046883..80048814-chr16:80056548..80058307,2	MCF-7	breast:
12	chr16:80049883..80052966-chr16:80055781..80058097,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261390	Chromatin interaction
ENSG00000260876	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1115722	0.81[EUR][1000 genomes]
rs11645922	0.96[EUR][1000 genomes]
rs12716881	0.89[EUR][1000 genomes]
rs12921255	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13333795	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1478505	0.86[EUR][1000 genomes]
rs1478506	0.86[EUR][1000 genomes]
rs2199645	0.80[EUR][1000 genomes]
rs4354957	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs4363873	0.84[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs4365299	0.91[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4402582	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4407073	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4500741	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4500745	0.85[EUR][1000 genomes]
rs4545830	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4888067	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4889068	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4889084	0.88[EUR][1000 genomes]
rs4889086	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs4889090	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs4889092	0.85[EUR][1000 genomes]
rs4889093	0.80[EUR][1000 genomes]
rs6564727	0.86[EUR][1000 genomes]
rs6564728	0.82[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs6564729	0.85[EUR][1000 genomes]
rs6564730	0.85[EUR][1000 genomes]
rs7184607	0.86[EUR][1000 genomes]
rs7185080	0.81[EUR][1000 genomes]
rs7192544	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs7192753	0.82[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7193465	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8050142	0.86[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8050160	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8050173	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8059251	0.88[EUR][1000 genomes]
rs9937844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9940390	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv573294	chr16:80005642-80131944	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889067	RFWD3	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80057000-80058400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr16:80057000-80059000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr16:80057200-80058200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr16:80057200-80058200	Enhancers	NH-A	brain
5	chr16:80057200-80058400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr16:80057200-80058400	Enhancers	Osteobl	bone
7	chr16:80057200-80058600	Enhancers	HUVEC	blood vessel
8	chr16:80057200-80059000	Enhancers	HSMMtube	muscle
9	chr16:80057200-80059600	Enhancers	Fetal Stomach	stomach
10	chr16:80057400-80059600	Enhancers	Stomach Smooth Muscle	stomach
11	chr16:80057600-80058200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr16:80057800-80058200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr16:80057800-80058200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:80057800-80058200	Enhancers	HMEC	breast
15	chr16:80057800-80058200	Enhancers	K562	blood
16	chr16:80057800-80058800	Flanking Active TSS	A549	lung
17	chr16:80057800-80059400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:80058000-80058200	Enhancers	NHEK	skin
19	chr16:80058000-80059400	Weak transcription	Colon Smooth Muscle	Colon
20	chr16:80058000-80060600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:80058000-80060600	Weak transcription	HSMM	muscle
22	chr16:80058000-80061000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:80058000-80061000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr16:80058000-80061000	Weak transcription	Placenta	Placenta
25	chr16:80058000-80061000	Weak transcription	Small Intestine	intestine
26	chr16:80058000-80061200	Weak transcription	Right Atrium	heart
27	chr16:80058000-80062200	Weak transcription	Esophagus	oesophagus

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