Variant report

Variant	rs549643140
Chromosome Location	chr3:48485128-48485129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48484948-48485307	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:48484988-48485196	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:48484670-48485413	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:48484910-48485345	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:48484036-48485400	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:48485006-48485247	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:48484863-48485286	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:48485060-48485350	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:48484919-48485229	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:48484059-48485410	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:48484973-48485239	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr3:48485047-48485298	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:48485085-48485317	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:48485050-48485245	K562	blood:	n/a	n/a
15	POLR2A	chr3:48484943-48485879	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:48461352..48463314-chr3:48484246..48486227,2	MCF-7	breast:
2	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
3	chr3:48472201..48473721-chr3:48483082..48485224,2	MCF-7	breast:
4	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:
5	chr3:48228273..48230987-chr3:48484727..48487110,2	K562	blood:

No data

Variant related genes	Relation type
CCDC51	TF binding region
ATRIP	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000164045	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv965164	chr3:48485079-48485579	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48482600-48487200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48482600-48487200	Weak transcription	Right Atrium	heart
3	chr3:48482600-48487400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:48482600-48487600	Weak transcription	Ovary	ovary
5	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:48483400-48485200	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr3:48483400-48486200	Strong transcription	Gastric	stomach
8	chr3:48483400-48486200	Strong transcription	Left Ventricle	heart
9	chr3:48483400-48486200	Strong transcription	Osteobl	bone
10	chr3:48483400-48486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:48483400-48486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:48483400-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:48483400-48486400	Strong transcription	Brain Anterior Caudate	brain
14	chr3:48483400-48486400	Strong transcription	Esophagus	oesophagus
15	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:48483600-48485200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:48483600-48485200	Strong transcription	Fetal Lung	lung
21	chr3:48483600-48485200	Strong transcription	Right Ventricle	heart
22	chr3:48483600-48486000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:48483600-48486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:48483600-48486200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:48483600-48486200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:48483600-48486200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:48483600-48486200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:48483600-48486200	Strong transcription	Fetal Thymus	thymus
29	chr3:48483600-48486200	Strong transcription	Lung	lung
30	chr3:48483600-48486400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:48483600-48486400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:48483600-48486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:48483600-48486400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:48483600-48486400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:48483600-48486400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:48483600-48486400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:48483600-48486400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:48483600-48486400	Strong transcription	Adipose Nuclei	Adipose
39	chr3:48483600-48486400	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:48483600-48486400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr3:48483600-48486400	Strong transcription	Colon Smooth Muscle	Colon
42	chr3:48483600-48486400	Strong transcription	Placenta	Placenta
43	chr3:48483600-48486400	Strong transcription	Pancreas	Pancrea
44	chr3:48483600-48486400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:48483600-48486400	Strong transcription	NH-A	brain
46	chr3:48483600-48486600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:48483600-48486600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:48483600-48486600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:48483600-48486600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:48483600-48487000	Strong transcription	Brain Germinal Matrix	brain

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