Variant report

Variant	rs558964541
Chromosome Location	chr3:46940654-46940655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:46940604-46940693	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:46940628-46940892	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:46938433-46940961	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46935290..46938710-chr3:46938764..46942918,5	K562	blood:
2	chr3:46924894..46926955-chr3:46938452..46941314,2	K562	blood:
3	chr3:46939682..46941906-chr3:46942383..46946161,3	K562	blood:
4	chr3:46939682..46941423-chr3:46942383..46944944,2	K562	blood:
5	chr3:46858188..46860125-chr3:46939783..46942119,2	K562	blood:

No data

Variant related genes	Relation type
PTH1R	TF binding region
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	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
12	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
13	esv3357520	chr3:46939998-46942796	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46934400-46951000	Weak transcription	Psoas Muscle	Psoas
2	chr3:46934600-46949400	Weak transcription	Fetal Kidney	kidney
3	chr3:46939400-46940800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr3:46939400-46941400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr3:46939400-46941600	Enhancers	Spleen	Spleen
6	chr3:46939600-46940800	Enhancers	Fetal Heart	heart
7	chr3:46939600-46941400	Bivalent Enhancer	Fetal Stomach	stomach
8	chr3:46939600-46941800	Enhancers	Fetal Lung	lung
9	chr3:46939600-46945000	Weak transcription	K562	blood
10	chr3:46939800-46940800	Enhancers	Primary B cells from cord blood	blood
11	chr3:46939800-46940800	Bivalent Enhancer	Fetal Thymus	thymus
12	chr3:46939800-46940800	Enhancers	Lung	lung
13	chr3:46940000-46940800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:46940000-46940800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
15	chr3:46940000-46940800	Enhancers	Gastric	stomach
16	chr3:46940000-46941600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:46940000-46941800	Enhancers	Right Atrium	heart
18	chr3:46940200-46941000	Enhancers	HUVEC	blood vessel
19	chr3:46940200-46941200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
20	chr3:46940200-46941200	Flanking Active TSS	HSMM	muscle
21	chr3:46940400-46940800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr3:46940400-46940800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr3:46940400-46940800	Enhancers	Left Ventricle	heart
24	chr3:46940400-46941000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:46940400-46941000	Bivalent Enhancer	Ovary	ovary
26	chr3:46940400-46941800	Enhancers	Brain Substantia Nigra	brain
27	chr3:46940400-46942000	Enhancers	Brain Angular Gyrus	brain
28	chr3:46940400-46942000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:46940400-46942000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:46940400-46942000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:46940400-46945000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:46940400-46950800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:46940600-46940800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
34	chr3:46940600-46940800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:46940600-46940800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:46940600-46940800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:46940600-46940800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:46940600-46940800	Bivalent Enhancer	Placenta	Placenta
39	chr3:46940600-46940800	Active TSS	HSMMtube	muscle
40	chr3:46940600-46941000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
41	chr3:46940600-46941400	Enhancers	Brain Germinal Matrix	brain
42	chr3:46940600-46941400	Enhancers	Right Ventricle	heart
43	chr3:46940600-46941800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:46940600-46942000	Enhancers	Brain Anterior Caudate	brain
45	chr3:46940600-46942000	Enhancers	Brain Cingulate Gyrus	brain
46	chr3:46940600-46942000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr3:46940600-46942200	Enhancers	Brain Hippocampus Middle	brain
48	chr3:46940600-46943000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:46940600-46944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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