Variant report

Variant	rs562180245
Chromosome Location	chr3:49726547-49726548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:232)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:232 , 50 per page) page: 1 2 3 4 5

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	FOXM1	chr3:49726327-49727107	GM12878	blood:	n/a	n/a
3	PML	chr3:49726356-49727238	K562	blood:	n/a	n/a
4	POLR2A	chr3:49726141-49727671	K562	blood:	n/a	n/a
5	POLR2A	chr3:49726435-49727248	U87	brain:	n/a	n/a
6	HEY1	chr3:49725970-49728370	K562	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	TCF12	chr3:49725698-49726619	HepG2	liver:	n/a	n/a
11	MYC	chr3:49726407-49726617	K562	blood:	n/a	n/a
12	POLR2A	chr3:49725260-49727210	HepG2	liver:	n/a	n/a
13	GATA1	chr3:49726234-49727056	PBDE	blood:	n/a	n/a
14	TBP	chr3:49726126-49727635	K562	blood:	n/a	n/a
15	JUND	chr3:49726455-49727100	HepG2	liver:	n/a	n/a
16	POU2F2	chr3:49725490-49727712	GM12891	blood:	n/a	n/a
17	TAL1	chr3:49726192-49727757	K562	blood:	n/a	chr3:49727577-49727585
18	CBX3	chr3:49725844-49727257	K562	blood:	n/a	n/a
19	ZBTB33	chr3:49726378-49727233	GM12878	blood:	n/a	n/a
20	YY1	chr3:49726466-49727228	A549	lung:	n/a	chr3:49727196-49727205
21	POLR2A	chr3:49726309-49727223	K562	blood:	n/a	n/a
22	MAX	chr3:49726094-49727719	K562	blood:	n/a	chr3:49727216-49727225 chr3:49727194-49727204
23	ELF1	chr3:49726509-49726710	K562	blood:	n/a	n/a
24	MXI1	chr3:49726380-49728045	SK-N-SH	brain:	n/a	n/a
25	IRF1	chr3:49726294-49727158	K562	blood:	n/a	n/a
26	POLR2A	chr3:49726135-49727566	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr3:49726325-49726706	K562	blood:	n/a	n/a
28	POLR2A	chr3:49726437-49727198	K562	blood:	n/a	n/a
29	MAX	chr3:49726451-49726557	A549	lung:	n/a	n/a
30	NFIC	chr3:49726124-49726655	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:49726227-49726933	K562	blood:	n/a	n/a
32	CTCF	chr3:49726454-49726916	K562	blood:	n/a	n/a
33	STAT5A	chr3:49726446-49727249	GM12878	blood:	n/a	chr3:49727190-49727202
34	TEAD4	chr3:49726422-49727195	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:49726094-49727151	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:49726537-49727234	GM12891	blood:	n/a	n/a
37	MBD4	chr3:49726510-49727014	HepG2	liver:	n/a	n/a
38	POLR2A	chr3:49725648-49727364	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr3:49725923-49727464	Hela-S3	cervix:	n/a	n/a
40	PBX3	chr3:49726546-49727119	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:49724868-49727352	HepG2	liver:	n/a	n/a
42	ARID3A	chr3:49726435-49726638	K562	blood:	n/a	n/a
43	PAX5	chr3:49726468-49727291	GM12878	blood:	n/a	n/a
44	CEBPD	chr3:49726053-49727801	K562	blood:	n/a	chr3:49726130-49726141
45	POLR2A	chr3:49725469-49728622	GM12892	blood:	n/a	n/a
46	POLR2A	chr3:49725512-49727704	GM12892	blood:	n/a	n/a
47	GATA1	chr3:49726429-49726789	K562	blood:	n/a	n/a
48	CTCF	chr3:49726520-49726670	GM06990	blood:	n/a	n/a
49	HCFC1	chr3:49726051-49727787	Hela-S3	cervix:	n/a	n/a
50	SP1	chr3:49726361-49727282	A549	lung:	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	chr3:49724349..49727675-chr3:49755739..49757510,3	MCF-7	breast:
4	chr1:16970425..16971927-chr3:49726367..49727791,15	HCT-116	colon:
5	chr1:16969549..16972758-chr3:49725610..49728945,8	K562	blood:
6	chr3:49708866..49715375-chr3:49724746..49730407,6	K562	blood:
7	chr3:49724739..49727802-chr3:49735823..49739048,3	MCF-7	breast:
8	chr3:49711727..49717769-chr3:49722772..49726950,7	K562	blood:
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	chr1:16968825..16972400-chr3:49724902..49730445,9	MCF-7	breast:
14	chr3:49722536..49724153-chr3:49724898..49727146,2	MCF-7	breast:
15	chr3:49724901..49726999-chr3:49761086..49763587,3	MCF-7	breast:
16	chr1:16970617..16971914-chr3:49726307..49727625,5	Hela-S3	cervix:
17	chr3:49448668..49451033-chr3:49723995..49726731,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259970	TF binding region
RNF123	TF binding region
MST1	TF binding region
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000176020	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000173540	Chromatin interaction
ENSG00000186301	Chromatin interaction
ENSG00000215908	Chromatin interaction
ENSG00000164062	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	chr3:49724800-49726600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49724800-49726600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49724800-49726600	Weak transcription	NHDF-Ad	bronchial
4	chr3:49725000-49726600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:49725200-49728400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:49725400-49726800	Flanking Active TSS	Fetal Intestine Small	intestine
7	chr3:49725600-49726800	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr3:49725600-49726800	Flanking Active TSS	Dnd41	blood
9	chr3:49725600-49727200	Active TSS	Liver	Liver
10	chr3:49725800-49726800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr3:49726000-49726600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:49726000-49726600	Flanking Active TSS	Hela-S3	cervix
13	chr3:49726000-49726800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:49726200-49726600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:49726200-49726600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:49726200-49726600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:49726200-49726600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr3:49726200-49726600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr3:49726200-49726600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:49726200-49726600	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr3:49726200-49726600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:49726200-49726600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr3:49726200-49726600	Flanking Active TSS	Fetal Brain Female	brain
24	chr3:49726200-49726600	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr3:49726200-49726600	Enhancers	Fetal Lung	lung
26	chr3:49726200-49726600	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:49726200-49726800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:49726200-49726800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49726200-49726800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:49726200-49726800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:49726200-49726800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr3:49726200-49726800	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr3:49726200-49726800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr3:49726200-49726800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr3:49726200-49726800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr3:49726200-49726800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:49726200-49726800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr3:49726200-49726800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:49726200-49726800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:49726200-49726800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr3:49726200-49726800	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr3:49726200-49726800	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr3:49726200-49726800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr3:49726200-49726800	Flanking Active TSS	Fetal Thymus	thymus
45	chr3:49726200-49726800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr3:49726200-49726800	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr3:49726200-49726800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:49726200-49726800	Flanking Bivalent TSS/Enh	HepG2	liver
49	chr3:49726200-49726800	Flanking Active TSS	K562	blood
50	chr3:49726200-49726800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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