Variant report

Variant	rs558308250
Chromosome Location	chr3:191047042-191047043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:190999845..191001643-chr3:191046703..191048798,2	MCF-7	breast:
2	chr3:191032916..191035495-chr3:191046200..191047748,2	MCF-7	breast:
3	chr16:8962585..8963523-chr3:191046236..191047148,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GMNC-5	chr3:191046593-191047101	NONHSAT093964

Variant related genes	Relation type
ENSG00000261481	Chromatin interaction
ENSG00000188958	Chromatin interaction
ENSG00000153048	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1851611	chr3:191028147-191073560	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv4169	chr3:191036298-191063465	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv3325773	chr3:191046083-191048631	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv10370	chr3:191046223-191049560	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191046200-191049200	Active TSS	Brain Angular Gyrus	brain
2	chr3:191046200-191049800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:191046200-191049800	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:191046400-191048200	Active TSS	Rectal Smooth Muscle	rectum
5	chr3:191046400-191048400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:191046400-191048600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:191046400-191048600	Active TSS	Brain Cingulate Gyrus	brain
8	chr3:191046400-191048600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:191046400-191048800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:191046400-191049800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr3:191046600-191047200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr3:191046600-191047800	Bivalent/Poised TSS	Primary T cells fromperipheralblood	blood
13	chr3:191046600-191047800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr3:191046600-191047800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
15	chr3:191046600-191047800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:191046600-191048000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:191046600-191048200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr3:191046600-191048200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:191046600-191048200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:191046600-191048800	Active TSS	Fetal Muscle Trunk	muscle
21	chr3:191046600-191049000	Active TSS	Colonic Mucosa	Colon
22	chr3:191046600-191049000	Active TSS	Fetal Intestine Large	intestine
23	chr3:191046600-191049000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:191046600-191049000	Active TSS	Left Ventricle	heart
25	chr3:191046600-191049200	Active TSS	HSMM	muscle
26	chr3:191046600-191049600	Active TSS	HSMMtube	muscle
27	chr3:191046600-191049800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:191046600-191049800	Active TSS	Ovary	ovary
29	chr3:191046600-191049800	Active TSS	Right Ventricle	heart
30	chr3:191046600-191050000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:191046600-191050200	Active TSS	Psoas Muscle	Psoas
32	chr3:191046600-191050600	Active TSS	Aorta	Aorta
33	chr3:191046600-191050600	Active TSS	Right Atrium	heart
34	chr3:191046800-191047200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:191046800-191047200	Active TSS	Primary hematopoietic stem cells	blood
36	chr3:191046800-191047200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:191046800-191047200	Active TSS	Brain Germinal Matrix	brain
38	chr3:191046800-191047600	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
39	chr3:191046800-191047600	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr3:191046800-191047600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:191046800-191047800	Active TSS	Primary T cells from cord blood	blood
42	chr3:191046800-191048000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:191046800-191048000	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr3:191046800-191048200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:191046800-191048200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:191046800-191048200	Active TSS	Brain Substantia Nigra	brain
47	chr3:191046800-191048400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:191046800-191048400	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr3:191046800-191048400	Active TSS	Spleen	Spleen
50	chr3:191046800-191048600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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