Variant report

Variant	rs549506298
Chromosome Location	chr12:12716097-12716098
allele	C/T
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	CREB1	chr12:12715308-12716239	GM12878	blood:	n/a	n/a
2	RAD21	chr12:12715501-12717510	SK-N-SH	brain:	n/a	chr12:12717133-12717152 chr12:12717149-12717168
3	POLR2A	chr12:12715920-12716174	GM12891	blood:	n/a	n/a
4	MXI1	chr12:12715560-12716187	GM12878	blood:	n/a	n/a
5	JUND	chr12:12714010-12716138	K562	blood:	n/a	chr12:12715384-12715393 chr12:12715493-12715502
6	POLR2A	chr12:12715503-12716169	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr12:12713503-12716782	HepG2	liver:	n/a	n/a
8	TCF12	chr12:12715506-12716256	ECC-1	luminal epithelium:	n/a	n/a
9	ZBTB7A	chr12:12714188-12716298	ECC-1	luminal epithelium:	n/a	chr12:12715455-12715469 chr12:12714468-12714476 chr12:12715115-12715123
10	POLR2A	chr12:12715581-12716133	HepG2	liver:	n/a	n/a
11	SIN3A	chr12:12715557-12716195	H1-hESC	embryonic stem cell:	n/a	chr12:12715832-12715845
12	POLR2A	chr12:12715533-12716234	GM12892	blood:	n/a	n/a
13	RUNX3	chr12:12715478-12716102	GM12878	blood:	n/a	n/a
14	MAZ	chr12:12713940-12716143	K562	blood:	n/a	chr12:12714863-12714872 chr12:12714847-12714857
15	HEY1	chr12:12715454-12716260	HepG2	liver:	n/a	n/a
16	ZNF143	chr12:12715667-12716207	K562	blood:	n/a	chr12:12715810-12715820
17	JUND	chr12:12715270-12716317	SK-N-SH	brain:	n/a	chr12:12715384-12715393 chr12:12715493-12715502
18	CTCF	chr12:12715507-12717540	SK-N-SH	brain:	n/a	chr12:12717150-12717171 chr12:12717141-12717150 chr12:12717135-12717153 chr12:12717148-12717166 chr12:12715817-12715830
19	RXRA	chr12:12715376-12716133	SK-N-SH	brain:	n/a	chr12:12715521-12715530
20	POLR2A	chr12:12713986-12716119	HUVEC	blood vessel:	n/a	n/a
21	MBD4	chr12:12715894-12716348	HepG2	liver:	n/a	n/a
22	CHD2	chr12:12715153-12716215	Hela-S3	cervix:	n/a	n/a
23	CHD1	chr12:12711450-12716107	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:12715526-12716167	Hela-S3	cervix:	n/a	n/a
25	E2F4	chr12:12716094-12716235	MCF10A-Er-Src	breast:	n/a	n/a
26	RCOR1	chr12:12715464-12716141	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:12713382-12716397	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:12713620-12716156	GM18505	blood:	n/a	n/a
29	POLR2A	chr12:12715069-12716183	HepG2	liver:	n/a	n/a
30	SMC3	chr12:12715391-12717663	SK-N-SH	brain:	n/a	chr12:12717144-12717151 chr12:12717137-12717151
31	MAZ	chr12:12715059-12716171	HepG2	liver:	n/a	n/a
32	POLR2A	chr12:12715473-12716139	GM12878	blood:	n/a	n/a
33	TAF1	chr12:12715867-12716299	H1-neurons	neurons:	n/a	n/a
34	CREB1	chr12:12715319-12716180	HepG2	liver:	n/a	n/a
35	CTCF	chr12:12716020-12716170	HPAF	blood vessel:	n/a	n/a
36	ARID3A	chr12:12715585-12716186	HepG2	liver:	n/a	n/a
37	POLR2A	chr12:12713914-12716242	IMR90	lung:	n/a	n/a
38	CTCF	chr12:12715960-12716110	BJ	skin:	n/a	n/a
39	POLR2A	chr12:12715489-12716107	HCT-116	colon:	n/a	n/a
40	POLR2A	chr12:12715629-12716102	HepG2	liver:	n/a	n/a
41	EBF1	chr12:12716071-12716124	GM12878	blood:	n/a	n/a
42	MXI1	chr12:12713877-12716342	IMR90	lung:	n/a	n/a
43	MAZ	chr12:12714583-12716197	Hela-S3	cervix:	n/a	chr12:12714863-12714872 chr12:12714847-12714857
44	POLR2A	chr12:12715501-12717198	GM12878	blood:	n/a	n/a
45	RAD21	chr12:12715496-12716197	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr12:12715980-12716130	AG04450	lung:	n/a	n/a
47	GTF2F1	chr12:12715719-12716129	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr12:12715500-12716256	GM12892	blood:	n/a	n/a
49	SMC3	chr12:12715613-12716217	Hela-S3	cervix:	n/a	n/a
50	MTA3	chr12:12713388-12716723	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:12634486..12639853-chr12:12714024..12717789,5	K562	blood:
2	chr12:12713858..12718896-chr12:12719623..12723320,7	MCF-7	breast:
3	chr12:12710433..12719642-chr12:12755652..12767678,23	MCF-7	breast:
4	chr12:12712251..12716973-chr12:12867058..12873344,10	MCF-7	breast:
5	chr12:12549500..12552302-chr12:12715831..12718057,2	MCF-7	breast:
6	chr12:12714157..12716777-chr12:12764288..12766468,3	MCF-7	breast:
7	chr12:12712910..12717920-chr12:12867983..12871802,5	K562	blood:
8	chr12:12657878..12659784-chr12:12714344..12718404,3	K562	blood:
9	chr12:12714451..12716184-chr12:12937424..12940263,2	MCF-7	breast:
10	chr12:12713075..12717194-chr12:12718362..12721939,6	K562	blood:
11	chr12:12715374..12716942-chr12:12773209..12776027,2	MCF-7	breast:
12	chr12:12711165..12717532-chr12:12865354..12880919,24	MCF-7	breast:
13	chr12:12715613..12717543-chr12:12816506..12818729,2	K562	blood:
14	chr12:12713736..12716645-chr12:14925588..14929665,3	MCF-7	breast:
15	chr12:12713891..12716367-chr3:161087265..161090021,2	MCF-7	breast:
16	chr12:12713685..12716948-chr12:12760123..12768151,9	K562	blood:
17	chr12:12713534..12716816-chr12:12876902..12880504,5	K562	blood:
18	chr12:12507988..12510235-chr12:12714031..12716523,2	MCF-7	breast:
19	chr12:12714508..12716169-chr12:12878232..12880566,3	K562	blood:
20	chr12:12601826..12603513-chr12:12715714..12717891,2	MCF-7	breast:

Variant related genes	Relation type
DUSP16	TF binding region
ENSG00000256658	Chromatin interaction
ENSG00000240424	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000178878	Chromatin interaction
ENSG00000255670	Chromatin interaction
ENSG00000111269	Chromatin interaction
ENSG00000246705	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000205791	Chromatin interaction
ENSG00000111276	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	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3325054	chr12:12713710-12717058	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv8922	chr12:12714292-12716467	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
6	esv3432721	chr12:12714335-12716833	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12711600-12716200	Active TSS	Liver	Liver
2	chr12:12711600-12716200	Active TSS	Duodenum Mucosa	Duodenum
3	chr12:12711600-12716200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr12:12712000-12716200	Active TSS	Fetal Intestine Small	intestine
5	chr12:12712200-12716200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:12712600-12716200	Active TSS	NHLF	lung
7	chr12:12712800-12716200	Active TSS	Brain Cingulate Gyrus	brain
8	chr12:12712800-12716400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:12712800-12716400	Active TSS	Fetal Muscle Trunk	muscle
10	chr12:12712800-12716400	Active TSS	Right Atrium	heart
11	chr12:12712800-12716800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:12713000-12716200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:12713000-12716200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:12713000-12716200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:12713200-12716200	Active TSS	Brain Hippocampus Middle	brain
16	chr12:12713200-12716400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr12:12713200-12716600	Active TSS	Brain Angular Gyrus	brain
18	chr12:12713400-12716400	Active TSS	Aorta	Aorta
19	chr12:12713400-12716400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr12:12713400-12716400	Active TSS	Psoas Muscle	Psoas
21	chr12:12713400-12716400	Active TSS	Right Ventricle	heart
22	chr12:12713600-12716200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:12713600-12716200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:12713600-12716200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:12713600-12716200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:12713600-12716200	Active TSS	Lung	lung
27	chr12:12713600-12716200	Active TSS	Pancreas	Pancrea
28	chr12:12713600-12716400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:12713600-12716800	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr12:12713800-12716200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:12713800-12716200	Active TSS	Left Ventricle	heart
32	chr12:12713800-12716200	Active TSS	Ovary	ovary
33	chr12:12713800-12716200	Active TSS	HSMM	muscle
34	chr12:12713800-12716200	Active TSS	HSMMtube	muscle
35	chr12:12713800-12716200	Active TSS	NHDF-Ad	bronchial
36	chr12:12713800-12716200	Active TSS	NHEK	skin
37	chr12:12713800-12716400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:12713800-12716600	Active TSS	Brain Substantia Nigra	brain
39	chr12:12713800-12716800	Active TSS	Small Intestine	intestine
40	chr12:12714000-12716200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:12714000-12716200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:12714000-12716200	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr12:12714000-12716200	Active TSS	Placenta Amnion	Placenta Amnion
44	chr12:12714000-12716200	Active TSS	Rectal Smooth Muscle	rectum
45	chr12:12714000-12716400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:12714000-12716600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:12714200-12716200	Active TSS	Esophagus	oesophagus
48	chr12:12714200-12716200	Active TSS	Fetal Lung	lung
49	chr12:12714400-12716200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:12714400-12716200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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