Variant report

Variant	rs138168709
Chromosome Location	chr3:49727180-49727181
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:298)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:298 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49726445-49727200	K562	blood:	n/a	n/a
2	PML	chr3:49726356-49727238	K562	blood:	n/a	n/a
3	POLR2A	chr3:49726141-49727671	K562	blood:	n/a	n/a
4	POLR2A	chr3:49726435-49727248	U87	brain:	n/a	n/a
5	HEY1	chr3:49725970-49728370	K562	blood:	n/a	n/a
6	ELF1	chr3:49726646-49727253	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49726475-49727258	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:49726360-49727681	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:49726252-49727452	PFSK-1	brain:	n/a	n/a
10	MAZ	chr3:49726792-49727222	Hela-S3	cervix:	n/a	chr3:49727194-49727204
11	POLR2A	chr3:49726711-49727262	A549	lung:	n/a	n/a
12	CHD2	chr3:49726841-49727189	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr3:49726849-49727389	K562	blood:	n/a	chr3:49726945-49726954
14	CHD2	chr3:49726690-49727463	Hela-S3	cervix:	n/a	n/a
15	GABPA	chr3:49726811-49727265	MCF-7	breast:	n/a	chr3:49726945-49726954
16	POLR2A	chr3:49725260-49727210	HepG2	liver:	n/a	n/a
17	TBP	chr3:49726707-49727230	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr3:49726126-49727635	K562	blood:	n/a	n/a
19	RCOR1	chr3:49726554-49727187	GM12878	blood:	n/a	n/a
20	GABPA	chr3:49726865-49727197	Hela-S3	cervix:	n/a	chr3:49726945-49726954
21	POU2F2	chr3:49725490-49727712	GM12891	blood:	n/a	n/a
22	MXI1	chr3:49726783-49727300	Hela-S3	cervix:	n/a	n/a
23	TEAD4	chr3:49726710-49727257	H1-hESC	embryonic stem cell:	n/a	n/a
24	HMGN3	chr3:49726983-49727231	K562	blood:	n/a	n/a
25	TAL1	chr3:49726192-49727757	K562	blood:	n/a	chr3:49727577-49727585
26	CBX3	chr3:49725844-49727257	K562	blood:	n/a	n/a
27	TBP	chr3:49726716-49727198	HepG2	liver:	n/a	n/a
28	ZBTB33	chr3:49726378-49727233	GM12878	blood:	n/a	n/a
29	ETS1	chr3:49726801-49727290	GM12878	blood:	n/a	chr3:49727194-49727205 chr3:49726957-49726966
30	YY1	chr3:49726466-49727228	A549	lung:	n/a	chr3:49727196-49727205
31	TAF1	chr3:49726684-49727203	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr3:49726309-49727223	K562	blood:	n/a	n/a
33	MAX	chr3:49726094-49727719	K562	blood:	n/a	chr3:49727216-49727225 chr3:49727194-49727204
34	POLR2A	chr3:49726626-49727209	HEK293	kidney:	n/a	n/a
35	MXI1	chr3:49726380-49728045	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr3:49726135-49727566	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr3:49726437-49727198	K562	blood:	n/a	n/a
38	GABPA	chr3:49726869-49727387	MCF-7	breast:	n/a	chr3:49726945-49726954
39	POU2F2	chr3:49726685-49727271	GM12878	blood:	n/a	n/a
40	PAX5	chr3:49726681-49727309	GM12892	blood:	n/a	n/a
41	REST	chr3:49726651-49727201	PFSK-1	brain:	n/a	n/a
42	MAX	chr3:49726880-49727284	H1-hESC	embryonic stem cell:	n/a	chr3:49727216-49727225 chr3:49727194-49727204
43	POLR2A	chr3:49726595-49727188	K562	blood:	n/a	n/a
44	STAT5A	chr3:49726446-49727249	GM12878	blood:	n/a	chr3:49727190-49727202
45	TEAD4	chr3:49726422-49727195	H1-hESC	embryonic stem cell:	n/a	n/a
46	RUNX3	chr3:49726776-49727271	GM12878	blood:	n/a	n/a
47	MAX	chr3:49726929-49727201	ECC-1	luminal epithelium:	n/a	n/a
48	CTCF	chr3:49727120-49727270	NHEK	skin:	n/a	n/a
49	SIN3AK20	chr3:49726827-49727276	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:49726599-49727560	Hela-S3	cervix:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49710552..49715225-chr3:49718907..49727364,14	MCF-7	breast:
2	chr1:16970672..16971760-chr3:49726371..49727463,9	MCF-7	breast:
3	chr12:54674340..54674894-chr3:49726726..49727505,2	Hela-S3	cervix:
4	chr3:49724349..49727675-chr3:49755739..49757510,3	MCF-7	breast:
5	chr1:16970425..16971927-chr3:49726367..49727791,15	HCT-116	colon:
6	chr1:16969549..16972758-chr3:49725610..49728945,8	K562	blood:
7	chr3:49708866..49715375-chr3:49724746..49730407,6	K562	blood:
8	chr3:49724739..49727802-chr3:49735823..49739048,3	MCF-7	breast:
9	chr1:16964923..16974624-chr3:49722461..49732046,16	K562	blood:
10	chr3:49709764..49714141-chr3:49724462..49728582,8	MCF-7	breast:
11	chr3:49719547..49721441-chr3:49726309..49728909,2	K562	blood:
12	chr1:16969769..16972744-chr3:49724987..49728952,10	MCF-7	breast:
13	chr1:16840059..16842019-chr3:49726620..49728606,2	MCF-7	breast:
14	chr1:16968825..16972400-chr3:49724902..49730445,9	MCF-7	breast:
15	chr3:49727014..49727624-chr9:137217199..137217737,2	HCT-116	colon:
16	chr3:49715099..49716706-chr3:49727000..49728524,2	K562	blood:
17	chr1:16970617..16971914-chr3:49726307..49727625,5	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000259970	TF binding region
MST1	TF binding region
ENSG00000261135	Chromatin interaction
ENSG00000186301	Chromatin interaction
ENSG00000215908	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000176020	Chromatin interaction
ENSG00000206652	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	esv1825475	chr3:49722732-49734243	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
9	esv11181	chr3:49726377-49733587	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49725200-49728400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:49725600-49727200	Active TSS	Liver	Liver
3	chr3:49726200-49727200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr3:49726200-49727800	Active TSS	HSMM	muscle
5	chr3:49726200-49728000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:49726200-49728000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:49726200-49728000	Flanking Active TSS	Colonic Mucosa	Colon
8	chr3:49726400-49727400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:49726400-49727400	Active TSS	Brain Germinal Matrix	brain
10	chr3:49726400-49727400	Active TSS	Esophagus	oesophagus
11	chr3:49726400-49727600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:49726400-49727600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:49726400-49727600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:49726400-49727600	Active TSS	Aorta	Aorta
15	chr3:49726400-49727600	Active TSS	Brain Substantia Nigra	brain
16	chr3:49726400-49727600	Active TSS	Small Intestine	intestine
17	chr3:49726400-49727600	Active TSS	NHLF	lung
18	chr3:49726400-49727800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:49726400-49727800	Active TSS	Ovary	ovary
20	chr3:49726400-49728000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:49726400-49728000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:49726400-49728000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:49726400-49728000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:49726400-49728000	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:49726400-49728000	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr3:49726400-49728000	Active TSS	Fetal Kidney	kidney
27	chr3:49726400-49728000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr3:49726400-49728000	Active TSS	Psoas Muscle	Psoas
29	chr3:49726400-49728000	Active TSS	HSMMtube	muscle
30	chr3:49726600-49727200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:49726600-49727400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:49726600-49727400	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr3:49726600-49727400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:49726600-49727400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr3:49726600-49727400	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr3:49726600-49727400	Active TSS	Brain Hippocampus Middle	brain
37	chr3:49726600-49727400	Active TSS	Placenta	Placenta
38	chr3:49726600-49727400	Active TSS	Stomach Mucosa	stomach
39	chr3:49726600-49727400	Active TSS	Thymus	Thymus
40	chr3:49726600-49727600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr3:49726600-49727600	Active TSS	Brain Angular Gyrus	brain
42	chr3:49726600-49727600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:49726600-49727600	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:49726600-49727600	Active TSS	Fetal Brain Female	brain
45	chr3:49726600-49727600	Active TSS	Spleen	Spleen
46	chr3:49726600-49727800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:49726600-49727800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:49726600-49727800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:49726600-49727800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:49726600-49727800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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