Variant report

Variant	rs73149770
Chromosome Location	chr4:56230957-56230958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
2	chr4:56229418..56231762-chr4:56240098..56243784,4	MCF-7	breast:
3	chr4:56227263..56230972-chr4:56267777..56269959,3	K562	blood:
4	chr4:56228156..56231321-chr4:56259147..56264011,5	MCF-7	breast:
5	chr4:56229576..56232238-chr4:56250715..56253310,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLOCK-1	chr4:56230138-56231024	ENSG00000249700.1

Variant related genes	Relation type
ENSG00000249700	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs73147878	1.00[AMR][1000 genomes]
rs73149362	1.00[AMR][1000 genomes]
rs73149762	1.00[AMR][1000 genomes]
rs73149795	1.00[AMR][1000 genomes]
rs73149797	1.00[AMR][1000 genomes]
rs73149801	1.00[AMR][1000 genomes]
rs73151846	1.00[AMR][1000 genomes]
rs73151855	1.00[AMR][1000 genomes]
rs73151862	1.00[AMR][1000 genomes]
rs73151884	1.00[AMR][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	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213400-56233600	Weak transcription	Fetal Intestine Large	intestine
2	chr4:56213600-56242600	Weak transcription	Gastric	stomach
3	chr4:56213800-56231800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:56213800-56233600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:56213800-56239000	Weak transcription	Brain Germinal Matrix	brain
6	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
7	chr4:56214000-56231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:56214000-56237800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:56214000-56241800	Weak transcription	Colonic Mucosa	Colon
10	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:56215000-56235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:56219400-56238400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:56219600-56231000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:56220200-56231200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:56220800-56241400	Weak transcription	Primary T cells from cord blood	blood
16	chr4:56223400-56231400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:56225400-56231200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:56225600-56235400	Weak transcription	Right Ventricle	heart
19	chr4:56225600-56237800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:56225800-56231600	Weak transcription	Spleen	Spleen
21	chr4:56225800-56233000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:56225800-56235600	Weak transcription	Aorta	Aorta
23	chr4:56225800-56236800	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:56225800-56237400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:56225800-56238400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:56225800-56244800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:56225800-56244800	Weak transcription	Stomach Mucosa	stomach
28	chr4:56226000-56231600	Weak transcription	Right Atrium	heart
29	chr4:56226000-56233200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:56226000-56233800	Weak transcription	Left Ventricle	heart
31	chr4:56226000-56234400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:56226000-56236000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:56226000-56237200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:56226000-56238400	Weak transcription	Osteobl	bone
35	chr4:56226000-56238600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:56226000-56240400	Weak transcription	HSMM	muscle
37	chr4:56226000-56241200	Weak transcription	Esophagus	oesophagus
38	chr4:56226000-56245000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:56226000-56245000	Weak transcription	HSMMtube	muscle
40	chr4:56227600-56233000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:56227800-56238400	Weak transcription	Placenta	Placenta
42	chr4:56228000-56244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:56228400-56234400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:56228400-56245400	Weak transcription	K562	blood
45	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:56228600-56231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:56229400-56232000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:56229400-56237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:56229600-56233400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:56229800-56231800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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