Variant report

Variant	rs539732196
Chromosome Location	chr3:52000360-52000361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:51999719-52003632	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:52000308-52002203	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
2	chr3:51996322..51998656-chr3:51999527..52001457,4	MCF-7	breast:
3	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
4	chr3:51997248..52000056-chr3:52000079..52001783,2	MCF-7	breast:
5	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
6	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
7	chr3:51966649..51968588-chr3:51999482..52001370,2	K562	blood:

No data

Variant related genes	Relation type
PCBP4	TF binding region
ENSG00000090097	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000114767	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	esv3403794	chr3:52000337-52003085	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51988400-52000600	Weak transcription	Hela-S3	cervix
2	chr3:51990600-52000400	Weak transcription	Small Intestine	intestine
3	chr3:51990600-52000400	Weak transcription	HUVEC	blood vessel
4	chr3:51990600-52000800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:51990800-52000400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:51991000-52000400	Weak transcription	Stomach Mucosa	stomach
7	chr3:51991000-52000600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:51991200-52000400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:51991200-52000400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:51992800-52000400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:51993400-52000400	Weak transcription	Osteobl	bone
12	chr3:51994600-52000800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:51995000-52000400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:51995400-52000600	Enhancers	Left Ventricle	heart
15	chr3:51995600-52000400	Enhancers	Right Atrium	heart
16	chr3:51996200-52001000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:51996400-52000600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:51996600-52001200	Enhancers	Fetal Brain Male	brain
19	chr3:51996600-52001200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:51996800-52000400	Enhancers	Fetal Heart	heart
21	chr3:51997200-52000600	Weak transcription	Fetal Intestine Large	intestine
22	chr3:51997600-52000600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:51997800-52001200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:51998000-52000800	Enhancers	Pancreas	Pancrea
25	chr3:51998200-52000400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:51998400-52000600	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr3:51998400-52000600	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr3:51998400-52000800	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr3:51998400-52000800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:51998600-52000400	Enhancers	Colon Smooth Muscle	Colon
31	chr3:51998600-52001200	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr3:51998800-52000400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:51998800-52000600	Enhancers	Gastric	stomach
34	chr3:51998800-52000600	Weak transcription	Ovary	ovary
35	chr3:51999000-52000400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr3:51999000-52000800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr3:51999000-52000800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
38	chr3:51999000-52001200	Flanking Active TSS	Fetal Brain Female	brain
39	chr3:51999200-52000400	Enhancers	Fetal Kidney	kidney
40	chr3:51999200-52000600	Enhancers	Aorta	Aorta
41	chr3:51999200-52000800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
42	chr3:51999200-52001000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:51999200-52001200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:51999200-52001200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:51999400-52000400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:51999400-52000600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:51999400-52000800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:51999400-52000800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
49	chr3:51999400-52000800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr3:51999600-52000400	Flanking Active TSS	Brain Hippocampus Middle	brain

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