Variant report

Variant	rs112413178
Chromosome Location	chr2:74212267-74212268
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:74210765-74213232	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:74211225-74213109	NB4	blood:	n/a	n/a
3	CEBPD	chr2:74211462-74212420	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:74211329-74212784	A549	lung:	n/a	n/a
5	POLR2A	chr2:74211177-74212821	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:74210578-74212297	GM12892	blood:	n/a	n/a
7	PML	chr2:74210348-74212317	GM12878	blood:	n/a	n/a
8	MAX	chr2:74211578-74212441	SK-N-SH	brain:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74212007-74212018 chr2:74212007-74212018
9	TCF7L2	chr2:74210640-74212797	HCT-116	colon:	n/a	n/a
10	POLR2A	chr2:74210759-74213608	GM19193	blood:	n/a	n/a
11	JUND	chr2:74212186-74212322	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:74211241-74212713	HepG2	liver:	n/a	n/a
13	MAX	chr2:74211320-74212297	NB4	blood:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74211332-74211342 chr2:74212007-74212018 chr2:74212007-74212018
14	EP300	chr2:74210516-74212461	ECC-1	luminal epithelium:	n/a	chr2:74212012-74212028 chr2:74211731-74211747 chr2:74210842-74210858 chr2:74211646-74211659 chr2:74211611-74211620
15	MYC	chr2:74211237-74212388	MCF-7	breast:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74211332-74211342 chr2:74212007-74212018 chr2:74212007-74212018
16	POLR2A	chr2:74211545-74213099	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr2:74210469-74212298	MCF-7	breast:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74211332-74211342 chr2:74211170-74211180 chr2:74212007-74212018 chr2:74212007-74212018
18	E2F6	chr2:74210614-74212293	H1-hESC	embryonic stem cell:	n/a	chr2:74212028-74212040 chr2:74212028-74212037
19	CCNT2	chr2:74211347-74213049	K562	blood:	n/a	chr2:74211893-74211902 chr2:74212839-74212848 chr2:74212028-74212037
20	NR3C1	chr2:74211269-74212479	A549	lung:	n/a	chr2:74211663-74211676
21	EBF1	chr2:74212079-74212418	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:74211827-74212766	H1-neurons	neurons:	n/a	n/a
23	GABPA	chr2:74212031-74212484	SK-N-SH	brain:	n/a	chr2:74212137-74212146
24	POLR2A	chr2:74210597-74212385	MCF-7	breast:	n/a	n/a
25	TCF3	chr2:74211328-74212300	GM12878	blood:	n/a	chr2:74211559-74211572 chr2:74211823-74211839
26	TAF1	chr2:74212073-74212305	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr2:74211721-74212293	HCT-116	colon:	n/a	n/a
28	POLR2A	chr2:74211265-74213546	GM18526	blood:	n/a	n/a
29	CHD2	chr2:74211583-74213231	Hela-S3	cervix:	n/a	chr2:74212029-74212039
30	HA-E2F1	chr2:74211482-74213149	Hela-S3	cervix:	n/a	chr2:74212028-74212040 chr2:74212028-74212037
31	BHLHE40	chr2:74211363-74212283	K562	blood:	n/a	chr2:74212008-74212017 chr2:74211727-74211743 chr2:74211730-74211746 chr2:74211733-74211749 chr2:74211738-74211754 chr2:74212008-74212017
32	MYC	chr2:74210151-74213343	A549	lung:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74211332-74211342 chr2:74211170-74211180 chr2:74213042-74213061 chr2:74212007-74212018 chr2:74212007-74212018
33	POLR2A	chr2:74210733-74212841	A549	lung:	n/a	n/a
34	MYC	chr2:74211477-74212318	K562	blood:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74212007-74212018 chr2:74212007-74212018
35	POLR2A	chr2:74210667-74212281	HCT-116	colon:	n/a	n/a
36	JUND	chr2:74212171-74212354	HepG2	liver:	n/a	chr2:74212172-74212181
37	POLR2A	chr2:74211018-74213746	K562	blood:	n/a	n/a
38	HNF4A	chr2:74212013-74212336	HepG2	liver:	n/a	chr2:74212240-74212253 chr2:74212240-74212253 chr2:74212237-74212255
39	POLR2A	chr2:74210822-74213106	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYC	chr2:74211130-74212440	NB4	blood:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74211332-74211342 chr2:74211170-74211180 chr2:74212007-74212018 chr2:74212007-74212018
41	MAX	chr2:74211445-74212272	SK-N-SH	brain:	n/a	chr2:74211806-74211813 chr2:74212008-74212017 chr2:74212007-74212018 chr2:74212007-74212018
42	MYC	chr2:74212256-74212267	MCF-7	breast:	n/a	n/a
43	POLR2A	chr2:74211923-74212309	HepG2	liver:	n/a	n/a
44	POLR2A	chr2:74210840-74213762	GM15510	blood:	n/a	n/a
45	POLR2A	chr2:74212137-74212314	HepG2	liver:	n/a	n/a
46	HMGN3	chr2:74211320-74212339	K562	blood:	n/a	n/a
47	TCF12	chr2:74210486-74212510	ECC-1	luminal epithelium:	n/a	chr2:74210980-74210990
48	HNF4A	chr2:74212080-74212320	HepG2	liver:	n/a	chr2:74212240-74212253 chr2:74212240-74212253 chr2:74212237-74212255
49	POLR2A	chr2:74212164-74212317	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:74211948-74212365	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:74055188..74061210-chr2:74210942..74215230,5	K562	blood:
2	chr2:74210880..74212548-chr2:74372314..74375193,2	K562	blood:
3	chr2:74210581..74214263-chr2:74424560..74427104,3	K562	blood:
4	chr2:74210903..74212994-chr2:74431667..74434283,2	MCF-7	breast:
5	chr2:74210880..74213761-chr2:74373693..74375989,3	K562	blood:
6	chr2:74187365..74198553-chr2:74205167..74212961,17	MCF-7	breast:
7	chr11:133905199..133907855-chr2:74210970..74213610,2	MCF-7	breast:
8	chr2:74211217..74213609-chr2:74345958..74348496,2	MCF-7	breast:
9	chr2:74052797..74060455-chr2:74207744..74214705,21	MCF-7	breast:
10	chr2:74103145..74104933-chr2:74212158..74213816,2	K562	blood:
11	chr2:74151695..74161558-chr2:74205273..74215127,19	K562	blood:
12	chr2:74210159..74214364-chr2:74424247..74427320,6	MCF-7	breast:
13	chr2:74209442..74213118-chr2:74372270..74377274,6	MCF-7	breast:
14	chr2:74151187..74158039-chr2:74203173..74216266,29	MCF-7	breast:
15	chr11:8709045..8711792-chr2:74211303..74213379,2	MCF-7	breast:
16	chr2:74212004..74214263-chr2:74425033..74427104,2	K562	blood:
17	chr2:74152462..74158334-chr2:74210550..74216243,8	K562	blood:
18	chr14:75746098..75746964-chr2:74211481..74212299,2	Hela-S3	cervix:
19	chr2:74210101..74212862-chr2:74733390..74736109,2	K562	blood:
20	chr2:74071679..74074362-chr2:74210863..74213464,2	K562	blood:
21	chr2:74055452..74058450-chr2:74210942..74214913,3	K562	blood:
22	chr2:74209118..74215634-chr2:74424964..74427991,9	MCF-7	breast:
23	chr12:122235984..122238947-chr2:74211072..74214040,3	MCF-7	breast:
24	chr2:74209066..74214459-chr2:74345671..74349502,5	K562	blood:
25	chr2:74147649..74157677-chr2:74203379..74217813,34	MCF-7	breast:
26	chr2:74055755..74057848-chr2:74210321..74213795,3	MCF-7	breast:
27	chr2:74210601..74212361-chr2:74374459..74376721,2	MCF-7	breast:
28	chr2:74211059..74212577-chr2:74271171..74274101,2	MCF-7	breast:
29	chr2:74209017..74213063-chr2:74345530..74349441,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TET3-2	chr2:74212259-74212284	XLOC_001531

Variant related genes	Relation type
ENSG00000255989	TF binding region
DGUOK-AS1	TF binding region
ENSG00000065911	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000201876	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000271536	Chromatin interaction
ENSG00000115289	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000187605	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000254648	Chromatin interaction
ENSG00000204241	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000124356	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011177	chr2:74167343-74239905	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3444943	chr2:74210644-74214042	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv3391332	chr2:74211144-74213742	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3389183	chr2:74211269-74213817	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3405058	chr2:74211594-74213392	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr2:74210600-74213000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:74210800-74212800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:74210800-74213000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:74210800-74213000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:74210800-74213000	Active TSS	Colon Smooth Muscle	Colon
6	chr2:74210800-74213000	Active TSS	Gastric	stomach
7	chr2:74210800-74213000	Active TSS	Rectal Smooth Muscle	rectum
8	chr2:74211000-74212800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:74211000-74213000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:74211000-74213200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:74211200-74212800	Active TSS	Brain Cingulate Gyrus	brain
12	chr2:74211200-74212800	Active TSS	Fetal Intestine Large	intestine
13	chr2:74211200-74213200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:74211400-74212800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:74211400-74212800	Active TSS	Fetal Brain Female	brain
16	chr2:74211400-74212800	Active TSS	NHEK	skin
17	chr2:74211400-74213000	Active TSS	Aorta	Aorta
18	chr2:74211400-74213000	Active TSS	Duodenum Mucosa	Duodenum
19	chr2:74211400-74213000	Active TSS	Esophagus	oesophagus
20	chr2:74211400-74213000	Active TSS	HSMMtube	muscle
21	chr2:74211400-74213200	Active TSS	Small Intestine	intestine
22	chr2:74211600-74212800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:74211600-74212800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:74211600-74212800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:74211600-74212800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:74211600-74212800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr2:74211600-74212800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:74211600-74212800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:74211600-74212800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:74211600-74212800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:74211600-74212800	Weak transcription	Fetal Brain Male	brain
32	chr2:74211600-74212800	Active TSS	Fetal Intestine Small	intestine
33	chr2:74211600-74212800	Active TSS	Fetal Thymus	thymus
34	chr2:74211600-74212800	Active TSS	Left Ventricle	heart
35	chr2:74211600-74212800	Active TSS	Pancreas	Pancrea
36	chr2:74211600-74212800	Active TSS	Psoas Muscle	Psoas
37	chr2:74211600-74212800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr2:74211600-74212800	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr2:74211600-74212800	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr2:74211600-74212800	Active TSS	K562	blood
41	chr2:74211600-74213000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:74211600-74213000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr2:74211600-74213000	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr2:74211600-74213000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:74211600-74213000	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:74211600-74213000	Active TSS	Liver	Liver
47	chr2:74211600-74213000	Active TSS	Brain Germinal Matrix	brain
48	chr2:74211600-74213000	Active TSS	Lung	lung
49	chr2:74211600-74213000	Active TSS	Ovary	ovary
50	chr2:74211600-74213000	Active TSS	Placenta Amnion	Placenta Amnion

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