Variant report

Variant	rs553914666
Chromosome Location	chr12:121975676-121975677
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	MXI1	chr12:121973624-121976489	SK-N-SH	brain:	n/a	n/a
2	RUNX3	chr12:121973725-121975930	GM12878	blood:	n/a	n/a
3	HEY1	chr12:121975591-121975784	HepG2	liver:	n/a	chr12:121975613-121975628
4	POLR2A	chr12:121972301-121975787	GM12878	blood:	n/a	n/a
5	EBF1	chr12:121974358-121975769	GM12878	blood:	n/a	n/a
6	SMARCB1	chr12:121973841-121976449	Hela-S3	cervix:	n/a	n/a
7	ELF1	chr12:121973969-121975832	GM12878	blood:	n/a	chr12:121975821-121975830 chr12:121975526-121975538 chr12:121975106-121975118 chr12:121975222-121975233
8	RCOR1	chr12:121974559-121975676	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:121975413-121975730	A549	lung:	n/a	n/a
10	NFATC1	chr12:121975085-121975742	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:121974513-121975799	HCT-116	colon:	n/a	n/a
12	POLR2A	chr12:121973547-121975876	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:121973653-121976782	GM19193	blood:	n/a	n/a
14	CHD2	chr12:121974710-121975720	Hela-S3	cervix:	n/a	n/a
15	RELA	chr12:121973849-121975728	GM19193	blood:	n/a	n/a
16	POLR2A	chr12:121973609-121976415	GM18951	blood:	n/a	n/a
17	MAX	chr12:121974400-121975695	HCT-116	colon:	n/a	chr12:121975043-121975053 chr12:121975245-121975255
18	CTCF	chr12:121975636-121975686	GM10266	blood:	n/a	n/a
19	POLR2A	chr12:121974590-121976343	NB4	blood:	n/a	n/a
20	E2F6	chr12:121974535-121975856	A549	lung:	n/a	chr12:121975822-121975832 chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975738-121975750 chr12:121975528-121975537
21	MAZ	chr12:121973768-121976444	GM12878	blood:	n/a	chr12:121975043-121975053 chr12:121974080-121974090 chr12:121976078-121976088
22	MAZ	chr12:121974678-121976111	Hela-S3	cervix:	n/a	chr12:121975043-121975053 chr12:121976078-121976088
23	EGR1	chr12:121975004-121975824	K562	blood:	n/a	chr12:121975528-121975538 chr12:121975128-121975137 chr12:121975524-121975535 chr12:121975746-121975760 chr12:121975127-121975140 chr12:121975127-121975140 chr12:121975525-121975535 chr12:121975523-121975536
24	EBF1	chr12:121974952-121976122	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:121973761-121976612	GM12892	blood:	n/a	n/a
26	MAX	chr12:121973713-121977024	ECC-1	luminal epithelium:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121974080-121974090 chr12:121976078-121976088 chr12:121973741-121973751
27	YY1	chr12:121974887-121976404	GM12878	blood:	n/a	chr12:121975615-121975629 chr12:121975132-121975143 chr12:121975973-121975987 chr12:121975824-121975833 chr12:121975520-121975531 chr12:121975822-121975833 chr12:121976161-121976172 chr12:121975821-121975830 chr12:121975528-121975542 chr12:121975522-121975536 chr12:121976080-121976089
28	NFIC	chr12:121974305-121975827	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr12:121973946-121975930	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr12:121974530-121976003	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:121973711-121976427	GM12892	blood:	n/a	n/a
32	POLR2A	chr12:121973296-121976832	GM12878	blood:	n/a	n/a
33	E2F6	chr12:121975041-121975778	A549	lung:	n/a	chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975738-121975750 chr12:121975528-121975537
34	RELA	chr12:121974144-121975706	GM10847	blood:	n/a	n/a
35	POLR2A	chr12:121974854-121976257	ECC-1	luminal epithelium:	n/a	n/a
36	REST	chr12:121973568-121976423	H1-neurons	neurons:	n/a	chr12:121973990-121974003 chr12:121975043-121975056 chr12:121976004-121976014 chr12:121974811-121974821 chr12:121974313-121974333
37	CREB1	chr12:121973803-121975810	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:121972255-121975759	GM12891	blood:	n/a	n/a
39	SIN3A	chr12:121973896-121976198	H1-hESC	embryonic stem cell:	n/a	chr12:121976005-121976014 chr12:121973948-121973958 chr12:121975763-121975776
40	POLR2A	chr12:121974593-121976163	Hela-S3	cervix:	n/a	n/a
41	RELA	chr12:121974083-121975715	GM18951	blood:	n/a	n/a
42	POLR2A	chr12:121973451-121976845	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:121974727-121976082	HCT-116	colon:	n/a	n/a
44	MAX	chr12:121974098-121975866	A549	lung:	n/a	chr12:121975043-121975053 chr12:121975245-121975255
45	PAX5	chr12:121974090-121975814	GM12878	blood:	n/a	n/a
46	HA-E2F1	chr12:121974740-121976786	MCF-7	breast:	n/a	chr12:121975949-121975959 chr12:121975822-121975832 chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975738-121975750 chr12:121975528-121975537 chr12:121976110-121976120
47	EGR1	chr12:121974881-121975710	ECC-1	luminal epithelium:	n/a	chr12:121975528-121975538 chr12:121975128-121975137 chr12:121975524-121975535 chr12:121975127-121975140 chr12:121975127-121975140 chr12:121975525-121975535 chr12:121975523-121975536
48	RUNX3	chr12:121972246-121977055	GM12878	blood:	n/a	n/a
49	MYC	chr12:121974465-121976545	NB4	blood:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121976078-121976088
50	MAX	chr12:121974423-121976422	HepG2	liver:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121976078-121976088

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:121975669-121975719	AG09319	gingival:	n/a
2	chr12:121975669-121975719	MCF-7	breast:	n/a
3	chr12:121975669-121975719	SKMC	muscle:	n/a
4	chr12:121975669-121975719	HIPEpiC	eye:	n/a
5	chr12:121975669-121975719	GM19239	blood:	n/a
6	chr12:121975669-121975719	SK-N-SH	brain:	n/a
7	chr12:121975669-121975719	NB4	blood:	n/a
8	chr12:121975669-121975719	NH-A	brain:	n/a
9	chr12:121975669-121975719	PrEC	prostate:	n/a
10	chr12:121975669-121975719	BJ	skin:	n/a
11	chr12:121975669-121975719	HCM	heart:	n/a
12	chr12:121975669-121975719	SAEC	small airway:	n/a
13	chr12:121975669-121975719	HRPEpiC	eye:	n/a
14	chr12:121975669-121975719	A549	lung:	n/a
15	chr12:121975669-121975719	LNCaP	prostate:	n/a
16	chr12:121975669-121975719	Hela-S3	cervix:	n/a
17	chr12:121975669-121975719	PANC-1	pancreas:	n/a
18	chr12:121975669-121975719	GM12878	blood:	n/a
19	chr12:121975669-121975719	BE2_C	brain:	n/a
20	chr12:121975669-121975719	HUVEC	blood vessel:	n/a
21	chr12:121975669-121975719	NHDF-neo	bronchial:	n/a
22	chr12:121975669-121975719	AG09309	skin:	n/a
23	chr12:121975669-121975719	HNPCEpiC	eye:	n/a
24	chr12:121975669-121975719	H1-hESC	embryonic stem cell:	embryo
25	chr12:121975669-121975719	AG04450	lung:	fetal
26	chr12:121975669-121975719	HCF	heart:	n/a
27	chr12:121975669-121975719	HPAEpiC	pulmonary alveolar:	n/a
28	chr12:121975669-121975719	HAEpiC	amniotic membrane:	n/a
29	chr12:121975669-121975719	Caco-2	colon:	n/a
30	chr12:121975669-121975719	HCT-116	colon:	n/a
31	chr12:121975669-121975719	NHBE	bronchial:	n/a
32	chr12:121975669-121975719	HL-60	blood:	n/a
33	chr12:121975669-121975719	IMR90	lung:	fetal
34	chr12:121975669-121975719	ovcar-3	ovarian:	n/a
35	chr12:121975669-121975719	AoSMC	blood vessel:	n/a
36	chr12:121975669-121975719	T-47D	breast:	n/a
37	chr12:121975669-121975719	ECC-1	luminal epithelium:	n/a
38	chr12:121975669-121975719	HRE	kidney:	n/a
39	chr12:121975669-121975719	HRCEpiC	kidney:	n/a
40	chr12:121975669-121975719	HMEC	breast:	n/a
41	chr12:121975669-121975719	AG10803	skin:	n/a
42	chr12:121975669-121975719	NT2-D1	testis:	n/a
43	chr12:121975669-121975719	SK-N-MC	brain:	n/a
44	chr12:121975669-121975719	CMK	blood:	n/a
45	chr12:121975669-121975719	Hepatocyte	liver:	n/a
46	chr12:121975669-121975719	SK-N-SH_RA	brain:	n/a
47	chr12:121975669-121975719	U87	brain:	n/a
48	chr12:121975669-121975719	HEK293	kidney:	embryo
49	chr12:121975669-121975719	PFSK-1	brain:	n/a
50	chr12:121975669-121975719	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121973453..121977492-chr12:122016919..122020388,4	K562	blood:
2	chr12:121975169..121976051-chr12:122240783..122241487,2	NB4	blood:
3	chr12:121974674..121977649-chr12:122063134..122066400,4	MCF-7	breast:
4	chr12:121974857..121978322-chr12:122063131..122066228,6	MCF-7	breast:
5	chr12:121974542..121976684-chr12:122017365..122019196,2	MCF-7	breast:
6	chr12:121966142..121973158-chr12:121973289..121976781,9	MCF-7	breast:
7	chr12:121973525..121977245-chr12:122063799..122066216,4	K562	blood:
8	chr12:121975167..121976771-chr12:122063978..122066637,2	K562	blood:
9	chr12:121974972..121977558-chr12:122231894..122235040,4	MCF-7	breast:
10	chr12:121937924..121939615-chr12:121975554..121978350,2	MCF-7	breast:
11	chr12:121945860..121947775-chr12:121975322..121977515,3	MCF-7	breast:
12	chr12:121974472..121977117-chr12:122150068..122152069,2	MCF-7	breast:
13	chr12:121972742..121976523-chr12:121985100..121990052,4	K562	blood:
14	chr12:121973342..121977941-chr12:121987524..121992877,7	MCF-7	breast:
15	chr12:121974810..121976577-chr12:122237441..122239422,3	MCF-7	breast:
16	chr12:121975126..121978118-chr12:121985924..121988501,3	MCF-7	breast:

Variant related genes	Relation type
KDM2B	TF binding region
KDM2B	CpG island
ENSG00000139725	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000182500	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560457	chr12:121956483-121976176	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
4	esv3354947	chr12:121974194-121976742	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121973200-121976800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:121973400-121976800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:121973600-121976400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:121973600-121976400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:121973600-121976600	Flanking Active TSS	Colonic Mucosa	Colon
6	chr12:121973600-121976600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:121973600-121976800	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr12:121973800-121975800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:121973800-121975800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr12:121973800-121975800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
11	chr12:121973800-121976400	Flanking Active TSS	NH-A	brain
12	chr12:121973800-121976600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr12:121973800-121976800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:121974000-121975800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:121974000-121975800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr12:121974000-121975800	Flanking Active TSS	HUVEC	blood vessel
17	chr12:121974000-121976000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:121974000-121976200	Active TSS	Aorta	Aorta
19	chr12:121974000-121976200	Active TSS	Brain Anterior Caudate	brain
20	chr12:121974000-121976200	Active TSS	Colon Smooth Muscle	Colon
21	chr12:121974000-121976200	Active TSS	Fetal Brain Female	brain
22	chr12:121974000-121976200	Active TSS	Ovary	ovary
23	chr12:121974000-121976200	Active TSS	Psoas Muscle	Psoas
24	chr12:121974000-121976200	Active TSS	Rectal Smooth Muscle	rectum
25	chr12:121974000-121976400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:121974000-121976400	Active TSS	Right Atrium	heart
27	chr12:121974000-121976600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:121974000-121976600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:121974200-121976400	Active TSS	Left Ventricle	heart
30	chr12:121974200-121976400	Weak transcription	Dnd41	blood
31	chr12:121974200-121976600	Active TSS	Right Ventricle	heart
32	chr12:121974400-121976000	Active TSS	Esophagus	oesophagus
33	chr12:121974400-121976200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:121974400-121976200	Active TSS	Brain Angular Gyrus	brain
35	chr12:121974400-121976400	Active TSS	Brain Substantia Nigra	brain
36	chr12:121974400-121976800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr12:121974600-121975800	Flanking Active TSS	NHEK	skin
38	chr12:121974600-121976200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:121974600-121976200	Active TSS	Brain Cingulate Gyrus	brain
40	chr12:121974600-121976400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:121974600-121976400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:121974600-121976400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:121974600-121976400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:121974600-121976800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr12:121974800-121976000	Active TSS	A549	lung
46	chr12:121974800-121976200	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr12:121974800-121976200	Active TSS	Brain Hippocampus Middle	brain
48	chr12:121974800-121976200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:121974800-121976200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr12:121974800-121976200	Active TSS	Lung	lung

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