Variant report

Variant	rs58529346
Chromosome Location	chr3:46988356-46988357
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46942667..46944620-chr3:46986480..46988761,2	K562	blood:
2	chr3:46986646..46988898-chr3:47016265..47017961,2	K562	blood:
3	chr3:46985961..46989571-chr3:47058662..47060411,3	K562	blood:
4	chr3:46984582..46987726-chr3:46988178..46990594,3	K562	blood:
5	chr3:46987488..46994423-chr3:47016253..47019914,6	MCF-7	breast:
6	chr3:46986886..46990722-chr3:47020544..47025137,5	MCF-7	breast:
7	chr3:46734374..46736416-chr3:46987784..46989611,2	MCF-7	breast:
8	chr3:46983747..46991522-chr3:47014474..47023916,13	MCF-7	breast:
9	chr3:46987136..46991583-chr3:47027983..47031367,6	K562	blood:
10	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
11	chr3:46987457..46990723-chr3:46999774..47002993,3	MCF-7	breast:
12	chr3:46983597..46986093-chr3:46988070..46989778,2	MCF-7	breast:
13	chr3:46988088..46989870-chr3:47001912..47004802,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160801	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000178038	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs55633581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55646108	1.00[AMR][1000 genomes]
rs55727789	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55730344	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55832326	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56329054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57341796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58040348	1.00[AMR][1000 genomes]
rs58918862	1.00[AMR][1000 genomes]
rs59614145	1.00[AMR][1000 genomes]
rs59846120	1.00[AMR][1000 genomes]
rs60017851	1.00[AMR][1000 genomes]
rs60100816	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831407	1.00[AFR][1000 genomes]
rs73831409	1.00[AMR][1000 genomes]
rs73831411	1.00[AMR][1000 genomes]
rs73831412	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831414	1.00[AMR][1000 genomes]
rs73831415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831424	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831425	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831428	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831430	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831432	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831444	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831445	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831446	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831448	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831449	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831451	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831453	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831454	1.00[AMR][1000 genomes]
rs73831455	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831457	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831458	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831459	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831466	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831467	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831468	1.00[AMR][1000 genomes]
rs73831469	1.00[AMR][1000 genomes]
rs73831471	1.00[AMR][1000 genomes]
rs73831472	1.00[AMR][1000 genomes]
rs73831474	1.00[AMR][1000 genomes]
rs73831477	1.00[AMR][1000 genomes]
rs73831479	1.00[AMR][1000 genomes]
rs73831480	1.00[AMR][1000 genomes]
rs73831481	1.00[AMR][1000 genomes]
rs73831483	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46971200-46988400	Strong transcription	Dnd41	blood
2	chr3:46974000-46988600	Strong transcription	Primary T cells from cord blood	blood
3	chr3:46976200-46990200	Weak transcription	Fetal Brain Male	brain
4	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:46978000-46990600	Strong transcription	Fetal Stomach	stomach
6	chr3:46979400-46989200	Weak transcription	NHDF-Ad	bronchial
7	chr3:46979600-46994600	Genic enhancers	Fetal Thymus	thymus
8	chr3:46980200-46990800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:46982200-46989000	Weak transcription	HSMMtube	muscle
10	chr3:46982400-46988600	Enhancers	Stomach Mucosa	stomach
11	chr3:46982400-46989000	Weak transcription	Aorta	Aorta
12	chr3:46982600-46988600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:46982600-46988800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:46982600-46988800	Weak transcription	NHLF	lung
15	chr3:46982600-46989000	Weak transcription	Brain Germinal Matrix	brain
16	chr3:46982800-46992600	Enhancers	Left Ventricle	heart
17	chr3:46983000-46989400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:46983000-46992600	Enhancers	Small Intestine	intestine
19	chr3:46983200-46989400	Enhancers	HMEC	breast
20	chr3:46983200-46989600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:46983200-46992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr3:46983400-46991200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:46983600-46992600	Enhancers	Psoas Muscle	Psoas
24	chr3:46983600-46992600	Enhancers	Right Atrium	heart
25	chr3:46983600-46994000	Enhancers	HUVEC	blood vessel
26	chr3:46984000-46989200	Weak transcription	Fetal Brain Female	brain
27	chr3:46984000-46989400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:46984200-46989000	Genic enhancers	K562	blood
29	chr3:46984200-46996400	Enhancers	Liver	Liver
30	chr3:46984400-46989000	Enhancers	Esophagus	oesophagus
31	chr3:46984800-46989200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:46984800-46989400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:46985000-46988800	Enhancers	Colonic Mucosa	Colon
34	chr3:46985000-46989400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:46985000-46989800	Enhancers	Brain Substantia Nigra	brain
36	chr3:46985000-46992000	Enhancers	Pancreas	Pancrea
37	chr3:46985000-46992600	Enhancers	Right Ventricle	heart
38	chr3:46985200-46989000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:46985200-46991800	Genic enhancers	Fetal Intestine Small	intestine
40	chr3:46985600-46988600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:46985600-46988600	Enhancers	Duodenum Mucosa	Duodenum
42	chr3:46985600-46989000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:46985600-46995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:46985800-46988400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:46985800-46988600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:46985800-46990000	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr3:46985800-46990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:46985800-46994200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:46986000-46988600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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