Variant report

Variant	rs6439609
Chromosome Location	chr3:135715022-135715023
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135713331..135715751-chr3:135731248..135733189,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs12630389	0.87[ASN][1000 genomes]
rs12632791	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12633805	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12637541	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13059064	0.83[ASN][1000 genomes]
rs13065499	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13069408	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072433	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072690	0.83[ASN][1000 genomes]
rs13072782	0.83[ASN][1000 genomes]
rs13075579	0.94[ASN][1000 genomes]
rs13078865	0.83[ASN][1000 genomes]
rs13092707	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13097267	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13100235	0.80[ASN][1000 genomes]
rs1523593	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1523599	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1523600	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16843560	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16843611	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140450	0.83[ASN][1000 genomes]
rs2177407	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2400649	0.83[ASN][1000 genomes]
rs34447526	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34683314	0.81[EUR][1000 genomes]
rs34706807	0.81[EUR][1000 genomes]
rs35097316	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35209948	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35264626	0.81[EUR][1000 genomes]
rs35532770	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946332	0.83[ASN][1000 genomes]
rs35961065	0.87[ASN][1000 genomes]
rs3946444	0.83[ASN][1000 genomes]
rs4075999	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4331626	0.82[ASN][1000 genomes]
rs4678224	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4678288	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4678432	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4678434	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4678435	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55873361	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56152207	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57594457	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60070757	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61791712	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61791714	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439603	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6439605	0.81[ASN][1000 genomes]
rs6439610	0.84[ASN][1000 genomes]
rs6439614	0.82[ASN][1000 genomes]
rs6439615	0.83[ASN][1000 genomes]
rs6439618	0.83[ASN][1000 genomes]
rs6439622	0.92[ASN][1000 genomes]
rs6439623	0.92[ASN][1000 genomes]
rs6439624	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6770366	0.81[ASN][1000 genomes]
rs6771950	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6775261	0.83[ASN][1000 genomes]
rs6779903	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6793273	0.86[ASN][1000 genomes]
rs6803786	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7433592	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7610302	0.83[ASN][1000 genomes]
rs7625177	0.83[ASN][1000 genomes]
rs7625607	0.85[ASN][1000 genomes]
rs7635621	0.83[ASN][1000 genomes]
rs7650079	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289501	0.80[ASN][1000 genomes]
rs940229	0.83[ASN][1000 genomes]
rs9682712	0.83[ASN][1000 genomes]
rs9758578	0.92[ASN][1000 genomes]
rs9846554	0.83[ASN][1000 genomes]
rs9852009	0.83[ASN][1000 genomes]
rs9852169	0.83[ASN][1000 genomes]
rs9856799	0.83[ASN][1000 genomes]
rs9868239	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135694000-135726600	Weak transcription	Esophagus	oesophagus
2	chr3:135701600-135720600	Weak transcription	Ovary	ovary
3	chr3:135704600-135716400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:135707000-135736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:135708200-135716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:135708200-135730200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:135709800-135717800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:135710000-135716800	Weak transcription	Psoas Muscle	Psoas
10	chr3:135710000-135726200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:135710000-135727200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:135710000-135737600	Weak transcription	Left Ventricle	heart
13	chr3:135710600-135715400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:135710800-135727600	Weak transcription	Aorta	Aorta
15	chr3:135711600-135717000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:135711600-135727800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:135711600-135731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:135711800-135727000	Weak transcription	Pancreas	Pancrea
19	chr3:135711800-135727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:135711800-135730400	Weak transcription	HSMM	muscle
21	chr3:135711800-135730400	Weak transcription	Osteobl	bone
22	chr3:135711800-135737600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:135712400-135721800	Weak transcription	NHDF-Ad	bronchial
24	chr3:135713800-135716200	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:135713800-135716600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:135714000-135716000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:135714000-135716000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:135714000-135716000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:135714000-135716000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:135714000-135716200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:135714000-135716400	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:135714000-135718000	Weak transcription	Brain Germinal Matrix	brain
33	chr3:135714000-135718800	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:135714000-135720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:135714000-135721200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:135714000-135729200	Weak transcription	NH-A	brain
37	chr3:135714000-135735600	Weak transcription	Fetal Heart	heart
38	chr3:135714200-135715600	Enhancers	Fetal Lung	lung
39	chr3:135714200-135716400	Weak transcription	NHEK	skin
40	chr3:135714200-135726000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:135714200-135737600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:135714400-135719600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:135714600-135715600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr3:135714600-135716000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:135714600-135717800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:135714600-135718200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:135714600-135726000	Weak transcription	Placenta	Placenta
48	chr3:135714800-135737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:135715000-135715400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:135715000-135716800	Enhancers	Rectal Smooth Muscle	rectum

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