Variant report

Variant	rs556105922
Chromosome Location	chr3:49726900-49726901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:515)
CpG islands
(count:61)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:515 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

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	CTCF	chr3:49726880-49727030	NHLF	lung:	n/a	n/a
3	FOXM1	chr3:49726327-49727107	GM12878	blood:	n/a	n/a
4	PML	chr3:49726356-49727238	K562	blood:	n/a	n/a
5	POLR2A	chr3:49726141-49727671	K562	blood:	n/a	n/a
6	POLR2A	chr3:49726435-49727248	U87	brain:	n/a	n/a
7	HEY1	chr3:49725970-49728370	K562	blood:	n/a	n/a
8	ELF1	chr3:49726646-49727253	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49726475-49727258	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:49726707-49727067	IMR90	lung:	n/a	n/a
11	POLR2A	chr3:49726360-49727681	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:49726252-49727452	PFSK-1	brain:	n/a	n/a
13	CTCF	chr3:49726860-49727010	AG04450	lung:	n/a	n/a
14	MAZ	chr3:49726792-49727222	Hela-S3	cervix:	n/a	chr3:49727194-49727204
15	POLR2A	chr3:49726711-49727262	A549	lung:	n/a	n/a
16	CHD2	chr3:49726841-49727189	H1-hESC	embryonic stem cell:	n/a	n/a
17	GABPA	chr3:49726849-49727389	K562	blood:	n/a	chr3:49726945-49726954
18	CHD2	chr3:49726690-49727463	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr3:49726811-49727265	MCF-7	breast:	n/a	chr3:49726945-49726954
20	CTCF	chr3:49726800-49726950	AG09309	skin:	n/a	n/a
21	POLR2A	chr3:49725260-49727210	HepG2	liver:	n/a	n/a
22	CTCF	chr3:49726780-49726930	GM12864	blood:	n/a	n/a
23	CTCF	chr3:49726860-49727010	Caco-2	colon:	n/a	n/a
24	TBP	chr3:49726707-49727230	H1-hESC	embryonic stem cell:	n/a	n/a
25	GATA1	chr3:49726234-49727056	PBDE	blood:	n/a	n/a
26	CTCF	chr3:49726810-49726993	GM13976	blood:	n/a	n/a
27	TBP	chr3:49726126-49727635	K562	blood:	n/a	n/a
28	RCOR1	chr3:49726554-49727187	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:49726617-49727154	MCF-7	breast:	n/a	n/a
30	JUND	chr3:49726455-49727100	HepG2	liver:	n/a	n/a
31	GABPA	chr3:49726865-49727197	Hela-S3	cervix:	n/a	chr3:49726945-49726954
32	CTCF	chr3:49726860-49727010	HA-sp	spinal cord:	n/a	n/a
33	ZBTB7A	chr3:49726846-49727080	HepG2	liver:	n/a	n/a
34	ELK1	chr3:49726801-49727113	Hela-S3	cervix:	n/a	n/a
35	POU2F2	chr3:49725490-49727712	GM12891	blood:	n/a	n/a
36	MXI1	chr3:49726783-49727300	Hela-S3	cervix:	n/a	n/a
37	TEAD4	chr3:49726710-49727257	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAL1	chr3:49726192-49727757	K562	blood:	n/a	chr3:49727577-49727585
39	RFX5	chr3:49726855-49727117	GM12878	blood:	n/a	n/a
40	CBX3	chr3:49725844-49727257	K562	blood:	n/a	n/a
41	FOXA1	chr3:49726840-49727083	T-47D	breast:	n/a	n/a
42	TBP	chr3:49726716-49727198	HepG2	liver:	n/a	n/a
43	CTCF	chr3:49726860-49727010	HCM	heart:	n/a	n/a
44	ZBTB33	chr3:49726378-49727233	GM12878	blood:	n/a	n/a
45	ETS1	chr3:49726801-49727290	GM12878	blood:	n/a	chr3:49727194-49727205 chr3:49726957-49726966
46	CTCF	chr3:49726840-49726990	HFF	foreskin:	n/a	n/a
47	YY1	chr3:49726466-49727228	A549	lung:	n/a	chr3:49727196-49727205
48	TAF1	chr3:49726684-49727203	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr3:49726309-49727223	K562	blood:	n/a	n/a
50	MAX	chr3:49726094-49727719	K562	blood:	n/a	chr3:49727216-49727225 chr3:49727194-49727204

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49726899-49726949	HRCEpiC	kidney:	n/a
2	chr3:49726899-49726949	K562	blood:	n/a
3	chr3:49726899-49726949	U87	brain:	n/a
4	chr3:49726899-49726949	Hela-S3	cervix:	n/a
5	chr3:49726899-49726949	AG09309	skin:	n/a
6	chr3:49726899-49726949	A549	lung:	n/a
7	chr3:49726899-49726949	Caco-2	colon:	n/a
8	chr3:49726899-49726949	AG10803	skin:	n/a
9	chr3:49726899-49726949	HL-60	blood:	n/a
10	chr3:49726899-49726949	BE2_C	brain:	n/a
11	chr3:49726899-49726949	HIPEpiC	eye:	n/a
12	chr3:49726899-49726949	AG09319	gingival:	n/a
13	chr3:49726899-49726949	HCM	heart:	n/a
14	chr3:49726899-49726949	SKMC	muscle:	n/a
15	chr3:49726899-49726949	HMEC	breast:	n/a
16	chr3:49726899-49726949	GM06990	blood:	n/a
17	chr3:49726899-49726949	HCPEpiC	choroid plexus:	n/a
18	chr3:49726899-49726949	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:49726899-49726949	AG04449	skin:	fetal
20	chr3:49726899-49726949	LNCaP	prostate:	n/a
21	chr3:49726899-49726949	NHBE	bronchial:	n/a
22	chr3:49726899-49726949	GM12878	blood:	n/a
23	chr3:49726899-49726949	GM19239	blood:	n/a
24	chr3:49726899-49726949	HCT-116	colon:	n/a
25	chr3:49726899-49726949	HEK293	kidney:	embryo
26	chr3:49726899-49726949	NH-A	brain:	n/a
27	chr3:49726899-49726949	HUVEC	blood vessel:	n/a
28	chr3:49726899-49726949	SK-N-MC	brain:	n/a
29	chr3:49726899-49726949	RPTEC	kidney:	n/a
30	chr3:49726899-49726949	Jurkat	blood:	n/a
31	chr3:49726899-49726949	HNPCEpiC	eye:	n/a
32	chr3:49726899-49726949	HCF	heart:	n/a
33	chr3:49726899-49726949	HEEpiC	esophagus:	n/a
34	chr3:49726899-49726949	Hepatocyte	liver:	n/a
35	chr3:49726899-49726949	AoSMC	blood vessel:	n/a
36	chr3:49726899-49726949	ovcar-3	ovarian:	n/a
37	chr3:49726899-49726949	ECC-1	luminal epithelium:	n/a
38	chr3:49726899-49726949	T-47D	breast:	n/a
39	chr3:49726899-49726949	GM12891	blood:	n/a
40	chr3:49726899-49726949	MCF10A-Er-Src	breast:	n/a
41	chr3:49726899-49726949	BJ	skin:	n/a
42	chr3:49726899-49726949	HAEpiC	amniotic membrane:	n/a
43	chr3:49726899-49726949	HRE	kidney:	n/a
44	chr3:49726899-49726949	ProgFib	skin:	n/a
45	chr3:49726899-49726949	CMK	blood:	n/a
46	chr3:49726899-49726949	PrEC	prostate:	n/a
47	chr3:49726899-49726949	PFSK-1	brain:	n/a
48	chr3:49726899-49726949	H1-hESC	embryonic stem cell:	embryo
49	chr3:49726899-49726949	GM12892	blood:	n/a
50	chr3:49726899-49726949	SK-N-SH_RA	brain:	n/a

(count:19 , 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	chr3:49711727..49717769-chr3:49722772..49726950,7	K562	blood:
10	chr1:16964923..16974624-chr3:49722461..49732046,16	K562	blood:
11	chr3:49709764..49714141-chr3:49724462..49728582,8	MCF-7	breast:
12	chr3:49719547..49721441-chr3:49726309..49728909,2	K562	blood:
13	chr1:16969769..16972744-chr3:49724987..49728952,10	MCF-7	breast:
14	chr1:16840059..16842019-chr3:49726620..49728606,2	MCF-7	breast:
15	chr1:16970648..16971367-chr3:49726608..49727129,5	MCF-7	breast:
16	chr1:16968825..16972400-chr3:49724902..49730445,9	MCF-7	breast:
17	chr3:49722536..49724153-chr3:49724898..49727146,2	MCF-7	breast:
18	chr3:49724901..49726999-chr3:49761086..49763587,3	MCF-7	breast:
19	chr1:16970617..16971914-chr3:49726307..49727625,5	Hela-S3	cervix:

No data

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000259970	TF binding region
MST1	TF binding region
ENSG00000259970	CpG island
MST1	CpG island
RNF123	CpG island
ENSG00000164068	Chromatin interaction
ENSG00000186301	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000173540	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000215908	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000176020	Chromatin interaction
ENSG00000173531	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv11877	chr3:49721171-49727086	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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	chr3:49726200-49727000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr3:49726200-49727000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:49726200-49727200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr3:49726200-49727800	Active TSS	HSMM	muscle
7	chr3:49726200-49728000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:49726200-49728000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:49726200-49728000	Flanking Active TSS	Colonic Mucosa	Colon
10	chr3:49726400-49727000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:49726400-49727400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:49726400-49727400	Active TSS	Brain Germinal Matrix	brain
13	chr3:49726400-49727400	Active TSS	Esophagus	oesophagus
14	chr3:49726400-49727600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:49726400-49727600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:49726400-49727600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:49726400-49727600	Active TSS	Aorta	Aorta
18	chr3:49726400-49727600	Active TSS	Brain Substantia Nigra	brain
19	chr3:49726400-49727600	Active TSS	Small Intestine	intestine
20	chr3:49726400-49727600	Active TSS	NHLF	lung
21	chr3:49726400-49727800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:49726400-49727800	Active TSS	Ovary	ovary
23	chr3:49726400-49728000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:49726400-49728000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr3:49726400-49728000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:49726400-49728000	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:49726400-49728000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:49726400-49728000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr3:49726400-49728000	Active TSS	Fetal Kidney	kidney
30	chr3:49726400-49728000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr3:49726400-49728000	Active TSS	Psoas Muscle	Psoas
32	chr3:49726400-49728000	Active TSS	HSMMtube	muscle
33	chr3:49726600-49727000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:49726600-49727000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49726600-49727000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:49726600-49727200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:49726600-49727400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:49726600-49727400	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr3:49726600-49727400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:49726600-49727400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr3:49726600-49727400	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr3:49726600-49727400	Active TSS	Brain Hippocampus Middle	brain
43	chr3:49726600-49727400	Active TSS	Placenta	Placenta
44	chr3:49726600-49727400	Active TSS	Stomach Mucosa	stomach
45	chr3:49726600-49727400	Active TSS	Thymus	Thymus
46	chr3:49726600-49727600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr3:49726600-49727600	Active TSS	Brain Angular Gyrus	brain
48	chr3:49726600-49727600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:49726600-49727600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:49726600-49727600	Active TSS	Fetal Brain Female	brain

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