Variant report

Variant	rs73835763
Chromosome Location	chr3:52282078-52282079
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52281218-52284689	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52281555-52284593	K562	blood:	n/a	n/a
3	POLR2A	chr3:52282064-52284490	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:52281575-52284260	U87	brain:	n/a	n/a
5	POLR2A	chr3:52282068-52282331	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:52279887-52284777	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:52281796-52284658	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:52281890-52284734	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr3:52281392-52284588	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:52281285-52284830	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:52281802-52282167	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:52281744-52284963	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:52281735-52284220	U87	brain:	n/a	n/a
14	POLR2A	chr3:52282054-52282346	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:52280752-52284781	A549	lung:	n/a	n/a
16	POLR2A	chr3:52282035-52284622	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:52281937-52284566	GM12892	blood:	n/a	n/a
18	POLR2A	chr3:52281882-52284077	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:52280316..52283002-chr3:52418190..52421140,2	K562	blood:
2	chr3:52279829..52282973-chr3:52309699..52312689,5	MCF-7	breast:
3	chr3:52278407..52281355-chr3:52281666..52283628,3	MCF-7	breast:

No data

Variant related genes	Relation type
PPM1M	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs55931436	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56263308	1.00[AMR][1000 genomes]
rs56332579	1.00[AMR][1000 genomes]
rs57265663	1.00[AMR][1000 genomes]
rs60063053	1.00[AMR][1000 genomes]
rs61589587	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61734625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61738522	1.00[AMR][1000 genomes]
rs6765965	1.00[AMR][1000 genomes]
rs6778451	1.00[AMR][1000 genomes]
rs6789826	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835708	1.00[AMR][1000 genomes]
rs73835711	1.00[AMR][1000 genomes]
rs73835764	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835767	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835771	0.87[AFR][1000 genomes]
rs73835772	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835773	1.00[AMR][1000 genomes]
rs73835774	1.00[AMR][1000 genomes]
rs73837050	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73837051	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73837056	1.00[AMR][1000 genomes]
rs73837058	1.00[AMR][1000 genomes]
rs73837574	1.00[AMR][1000 genomes]
rs73838346	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73838349	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7644241	1.00[AMR][1000 genomes]

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	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52279600-52287400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52280200-52287600	Weak transcription	HMEC	breast
3	chr3:52280200-52287800	Weak transcription	Small Intestine	intestine
4	chr3:52280200-52290000	Weak transcription	Ovary	ovary
5	chr3:52280400-52282200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52280400-52282200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr3:52280400-52282600	Weak transcription	Brain Angular Gyrus	brain
8	chr3:52280400-52282800	Weak transcription	Aorta	Aorta
9	chr3:52280400-52287000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52280400-52291200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:52280600-52282200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:52280600-52282400	Enhancers	Lung	lung
13	chr3:52280600-52282800	Weak transcription	NH-A	brain
14	chr3:52280600-52283000	Weak transcription	Fetal Intestine Large	intestine
15	chr3:52280600-52284400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52280600-52285000	Weak transcription	A549	lung
17	chr3:52280600-52287000	Weak transcription	HSMMtube	muscle
18	chr3:52280600-52287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:52280600-52288200	Weak transcription	Fetal Kidney	kidney
20	chr3:52280600-52290800	Weak transcription	Psoas Muscle	Psoas
21	chr3:52280600-52292400	Weak transcription	Fetal Heart	heart
22	chr3:52280800-52282200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:52280800-52282400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:52280800-52282800	Weak transcription	NHEK	skin
25	chr3:52280800-52287400	Weak transcription	K562	blood
26	chr3:52280800-52292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:52281000-52282800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:52281000-52282800	Weak transcription	HSMM	muscle
29	chr3:52281000-52283400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:52281000-52285200	Weak transcription	HUVEC	blood vessel
31	chr3:52281000-52287200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:52281000-52291800	Strong transcription	Fetal Intestine Small	intestine
33	chr3:52281200-52282200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:52281200-52282200	Weak transcription	Brain Anterior Caudate	brain
35	chr3:52281200-52282200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:52281200-52282200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:52281200-52282200	Weak transcription	Colonic Mucosa	Colon
38	chr3:52281200-52282200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:52281200-52282200	Weak transcription	Fetal Lung	lung
40	chr3:52281200-52282400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:52281200-52282400	Weak transcription	Right Ventricle	heart
42	chr3:52281200-52282600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:52281200-52282600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:52281200-52282600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:52281200-52282800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:52281200-52282800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr3:52281200-52283000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:52281200-52283000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
49	chr3:52281200-52283000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:52281200-52283400	Weak transcription	Stomach Mucosa	stomach

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