Variant report

Variant	rs561954001
Chromosome Location	chr12:121975233-121975234
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	E2F6	chr12:121974625-121975624	K562	blood:	n/a	chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975528-121975537
2	MXI1	chr12:121973624-121976489	SK-N-SH	brain:	n/a	n/a
3	MYC	chr12:121975194-121975383	HUVEC	blood vessel:	n/a	chr12:121975245-121975255
4	CTCF	chr12:121975197-121975234	GM12891	blood:	n/a	n/a
5	USF1	chr12:121975037-121975375	SK-N-SH_RA	brain:	n/a	chr12:121975134-121975150 chr12:121975245-121975256
6	POLR2A	chr12:121974688-121975416	K562	blood:	n/a	n/a
7	RUNX3	chr12:121973725-121975930	GM12878	blood:	n/a	n/a
8	YY1	chr12:121974787-121975491	HepG2	liver:	n/a	chr12:121975132-121975143
9	EP300	chr12:121974936-121975556	GM12878	blood:	n/a	n/a
10	E2F6	chr12:121974579-121975616	K562	blood:	n/a	chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975528-121975537
11	USF1	chr12:121975039-121975364	A549	lung:	n/a	chr12:121975134-121975150 chr12:121975245-121975256
12	POLR2A	chr12:121974995-121975294	Gliobla	brain:	n/a	n/a
13	PAX5	chr12:121975050-121975326	GM12891	blood:	n/a	n/a
14	USF1	chr12:121975118-121975358	K562	blood:	n/a	chr12:121975134-121975150 chr12:121975245-121975256
15	POLR2A	chr12:121974661-121975538	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr12:121972301-121975787	GM12878	blood:	n/a	n/a
17	MAX	chr12:121975082-121975358	K562	blood:	n/a	chr12:121975245-121975255
18	EBF1	chr12:121974358-121975769	GM12878	blood:	n/a	n/a
19	SMARCB1	chr12:121973841-121976449	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:121974880-121975458	HUVEC	blood vessel:	n/a	n/a
21	ELF1	chr12:121973969-121975832	GM12878	blood:	n/a	chr12:121975821-121975830 chr12:121975526-121975538 chr12:121975106-121975118 chr12:121975222-121975233
22	MBD4	chr12:121975023-121975408	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:121975013-121975675	GM12891	blood:	n/a	n/a
24	GABPA	chr12:121974790-121975521	MCF-7	breast:	n/a	n/a
25	ELF1	chr12:121974893-121975377	K562	blood:	n/a	chr12:121975106-121975118 chr12:121975222-121975233
26	RCOR1	chr12:121974559-121975676	Hela-S3	cervix:	n/a	n/a
27	UBTF	chr12:121975034-121975380	K562	blood:	n/a	n/a
28	POLR2A	chr12:121975119-121975300	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr12:121975044-121975617	GM12878	blood:	n/a	chr12:121975467-121975477
30	MAZ	chr12:121973926-121975373	K562	blood:	n/a	chr12:121975043-121975053 chr12:121974080-121974090
31	NFATC1	chr12:121975085-121975742	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:121974513-121975799	HCT-116	colon:	n/a	n/a
33	POLR2A	chr12:121973547-121975876	GM12892	blood:	n/a	n/a
34	POLR2A	chr12:121973653-121976782	GM19193	blood:	n/a	n/a
35	POLR2A	chr12:121974851-121975401	A549	lung:	n/a	n/a
36	CHD2	chr12:121974710-121975720	Hela-S3	cervix:	n/a	n/a
37	NR2F2	chr12:121974580-121975611	MCF-7	breast:	n/a	n/a
38	RELA	chr12:121973849-121975728	GM19193	blood:	n/a	n/a
39	POLR2A	chr12:121973609-121976415	GM18951	blood:	n/a	n/a
40	MAX	chr12:121974400-121975695	HCT-116	colon:	n/a	chr12:121975043-121975053 chr12:121975245-121975255
41	TAF1	chr12:121974776-121975383	HepG2	liver:	n/a	n/a
42	FOXM1	chr12:121973936-121975631	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:121974622-121975462	HepG2	liver:	n/a	n/a
44	POLR2A	chr12:121974864-121975508	A549	lung:	n/a	n/a
45	POLR2A	chr12:121974590-121976343	NB4	blood:	n/a	n/a
46	E2F6	chr12:121974535-121975856	A549	lung:	n/a	chr12:121975822-121975832 chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975738-121975750 chr12:121975528-121975537
47	HNF4A	chr12:121975037-121975274	HepG2	liver:	n/a	chr12:121975211-121975224 chr12:121975206-121975228 chr12:121975211-121975224
48	MAZ	chr12:121973768-121976444	GM12878	blood:	n/a	chr12:121975043-121975053 chr12:121974080-121974090 chr12:121976078-121976088
49	TBP	chr12:121974706-121975371	Hela-S3	cervix:	n/a	n/a
50	USF2	chr12:121975108-121975351	HepG2	liver:	n/a	chr12:121975134-121975150 chr12:121975245-121975256

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	chr12:121974472..121977117-chr12:122150068..122152069,2	MCF-7	breast:
11	chr12:121972742..121976523-chr12:121985100..121990052,4	K562	blood:
12	chr12:121973342..121977941-chr12:121987524..121992877,7	MCF-7	breast:
13	chr12:121974810..121976577-chr12:122237441..122239422,3	MCF-7	breast:
14	chr12:121975126..121978118-chr12:121985924..121988501,3	MCF-7	breast:

Variant related genes	Relation type
KDM2B	TF binding region
ENSG00000182500	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000256742	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:124 , 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	chr12:121973600-121975600	Flanking Active TSS	Fetal Muscle Leg	muscle
4	chr12:121973600-121976400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:121973600-121976400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:121973600-121976600	Flanking Active TSS	Colonic Mucosa	Colon
7	chr12:121973600-121976600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:121973600-121976800	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr12:121973800-121975600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:121973800-121975600	Flanking Active TSS	Placenta	Placenta
11	chr12:121973800-121975800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:121973800-121975800	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr12:121973800-121975800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
14	chr12:121973800-121976400	Flanking Active TSS	NH-A	brain
15	chr12:121973800-121976600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr12:121973800-121976800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:121974000-121975400	Flanking Active TSS	Osteobl	bone
18	chr12:121974000-121975800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:121974000-121975800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr12:121974000-121975800	Flanking Active TSS	HUVEC	blood vessel
21	chr12:121974000-121976000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:121974000-121976200	Active TSS	Aorta	Aorta
23	chr12:121974000-121976200	Active TSS	Brain Anterior Caudate	brain
24	chr12:121974000-121976200	Active TSS	Colon Smooth Muscle	Colon
25	chr12:121974000-121976200	Active TSS	Fetal Brain Female	brain
26	chr12:121974000-121976200	Active TSS	Ovary	ovary
27	chr12:121974000-121976200	Active TSS	Psoas Muscle	Psoas
28	chr12:121974000-121976200	Active TSS	Rectal Smooth Muscle	rectum
29	chr12:121974000-121976400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:121974000-121976400	Active TSS	Right Atrium	heart
31	chr12:121974000-121976600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:121974000-121976600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:121974200-121975400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr12:121974200-121975400	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr12:121974200-121975400	Enhancers	HSMMtube	muscle
36	chr12:121974200-121975600	Active TSS	Fetal Lung	lung
37	chr12:121974200-121976400	Active TSS	Left Ventricle	heart
38	chr12:121974200-121976400	Weak transcription	Dnd41	blood
39	chr12:121974200-121976600	Active TSS	Right Ventricle	heart
40	chr12:121974400-121975400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:121974400-121975600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:121974400-121975600	Flanking Active TSS	HepG2	liver
43	chr12:121974400-121976000	Active TSS	Esophagus	oesophagus
44	chr12:121974400-121976200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:121974400-121976200	Active TSS	Brain Angular Gyrus	brain
46	chr12:121974400-121976400	Active TSS	Brain Substantia Nigra	brain
47	chr12:121974400-121976800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr12:121974600-121975600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:121974600-121975600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:121974600-121975800	Flanking Active TSS	NHEK	skin

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