Variant report

Variant	rs560226580
Chromosome Location	chr12:104234309-104234310
allele	A/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	CEBPD	chr12:104234003-104234441	K562	blood:	n/a	n/a
2	EGR1	chr12:104234258-104234583	GM12878	blood:	n/a	chr12:104234375-104234389 chr12:104234376-104234387 chr12:104234376-104234387 chr12:104234371-104234393 chr12:104234377-104234387 chr12:104234375-104234388 chr12:104234376-104234390 chr12:104234377-104234387
3	EGR1	chr12:104234211-104236032	HCT-116	colon:	n/a	chr12:104235534-104235549 chr12:104234375-104234389 chr12:104234376-104234387 chr12:104235113-104235127 chr12:104234376-104234387 chr12:104235150-104235164 chr12:104235536-104235547 chr12:104235230-104235239 chr12:104234371-104234393 chr12:104235720-104235734 chr12:104235133-104235147 chr12:104234377-104234387 chr12:104234375-104234388 chr12:104234376-104234390 chr12:104235085-104235099 chr12:104235227-104235240 chr12:104235227-104235240 chr12:104234377-104234387
4	REST	chr12:104234039-104235378	H1-neurons	neurons:	n/a	chr12:104235302-104235315 chr12:104235366-104235375 chr12:104235191-104235204
5	MXI1	chr12:104233534-104236201	SK-N-SH	brain:	n/a	n/a
6	EGR1	chr12:104234183-104234560	K562	blood:	n/a	chr12:104234375-104234389 chr12:104234376-104234387 chr12:104234376-104234387 chr12:104234371-104234393 chr12:104234377-104234387 chr12:104234375-104234388 chr12:104234376-104234390 chr12:104234377-104234387
7	SIN3AK20	chr12:104233874-104236425	MCF-7	breast:	n/a	n/a
8	GATA3	chr12:104233966-104234340	T-47D	breast:	n/a	n/a
9	EBF1	chr12:104234208-104234638	GM12878	blood:	n/a	chr12:104234395-104234404 chr12:104234393-104234404 chr12:104234395-104234404 chr12:104234395-104234405
10	KAT2A	chr12:104234218-104235011	Hela-S3	cervix:	n/a	n/a
11	ZNF143	chr12:104234299-104234474	GM12878	blood:	n/a	n/a
12	MXI1	chr12:104233369-104236110	IMR90	lung:	n/a	n/a
13	EBF1	chr12:104234214-104234607	GM12878	blood:	n/a	chr12:104234395-104234404 chr12:104234393-104234404 chr12:104234395-104234404 chr12:104234395-104234405
14	MAX	chr12:104234176-104236277	A549	lung:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
15	POLR2A	chr12:104234238-104236223	Hela-S3	cervix:	n/a	n/a
16	MAX	chr12:104234283-104236007	K562	blood:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
17	RAD21	chr12:104234222-104234591	IMR90	lung:	n/a	chr12:104234577-104234591
18	POLR2A	chr12:104234139-104235191	IMR90	lung:	n/a	n/a
19	NFIC	chr12:104234128-104234582	GM12878	blood:	n/a	n/a
20	EGR1	chr12:104234021-104236169	HCT-116	colon:	n/a	chr12:104235534-104235549 chr12:104234375-104234389 chr12:104234376-104234387 chr12:104235113-104235127 chr12:104234376-104234387 chr12:104235150-104235164 chr12:104235536-104235547 chr12:104235230-104235239 chr12:104234371-104234393 chr12:104235720-104235734 chr12:104235133-104235147 chr12:104234377-104234387 chr12:104234375-104234388 chr12:104234376-104234390 chr12:104235085-104235099 chr12:104235227-104235240 chr12:104235227-104235240 chr12:104234377-104234387
21	NFATC1	chr12:104234220-104234574	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:104234279-104236028	H1-hESC	embryonic stem cell:	n/a	n/a
23	EGR1	chr12:104234249-104234445	GM12878	blood:	n/a	chr12:104234375-104234389 chr12:104234376-104234387 chr12:104234376-104234387 chr12:104234371-104234393 chr12:104234377-104234387 chr12:104234375-104234388 chr12:104234376-104234390 chr12:104234377-104234387
24	MAZ	chr12:104234025-104236471	IMR90	lung:	n/a	chr12:104235191-104235200 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
25	MAX	chr12:104234200-104236140	A549	lung:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
26	SMARCB1	chr12:104234246-104236215	Hela-S3	cervix:	n/a	n/a
27	ELF1	chr12:104234183-104235264	GM12878	blood:	n/a	chr12:104235066-104235078
28	EBF1	chr12:104234127-104235216	GM12878	blood:	n/a	chr12:104234395-104234404 chr12:104234393-104234404 chr12:104234395-104234404 chr12:104234395-104234405
29	MAX	chr12:104234092-104236104	HCT-116	colon:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
30	MAZ	chr12:104234270-104236011	K562	blood:	n/a	chr12:104235191-104235200 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
31	POLR2A	chr12:104233750-104236063	MCF10A-Er-Src	breast:	n/a	n/a
32	EGR1	chr12:104234207-104234542	K562	blood:	n/a	chr12:104234375-104234389 chr12:104234376-104234387 chr12:104234376-104234387 chr12:104234371-104234393 chr12:104234377-104234387 chr12:104234375-104234388 chr12:104234376-104234390 chr12:104234377-104234387
33	POLR2A	chr12:104234244-104235116	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104192525..104200371-chr12:104233987..104238967,10	MCF-7	breast:
2	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
3	chr12:104186150..104188258-chr12:104233575..104235121,2	K562	blood:
4	chr12:104211319..104217420-chr12:104233507..104236073,8	MCF-7	breast:
5	chr12:104219162..104221997-chr12:104232338..104234895,2	K562	blood:
6	chr12:104234047..104236214-chr12:104531313..104532962,2	MCF-7	breast:
7	chr12:104233429..104235958-chr12:104358438..104361946,3	MCF-7	breast:
8	chr12:104234073..104236683-chr12:104349820..104352847,3	K562	blood:
9	chr12:104186877..104189949-chr12:104233437..104236104,3	MCF-7	breast:
10	chr12:104233800..104236223-chr12:104679514..104682489,2	K562	blood:
11	chr12:104208263..104213427-chr12:104233273..104236383,5	K562	blood:
12	chr12:104234122..104238773-chr12:104347839..104352988,5	MCF-7	breast:
13	chr12:104233713..104237034-chr12:104348727..104352026,4	MCF-7	breast:
14	chr12:104233715..104236918-chr12:104321893..104325386,6	K562	blood:

Variant related genes	Relation type
ENSG00000257327	TF binding region
ENSG00000214198	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000257754	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000139372	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv3372343	chr12:104234047-104236595	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104231800-104235400	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:104231800-104236000	Active TSS	Rectal Smooth Muscle	rectum
3	chr12:104232000-104236000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:104232200-104235600	Active TSS	Aorta	Aorta
5	chr12:104232400-104235800	Active TSS	Colon Smooth Muscle	Colon
6	chr12:104232800-104234400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:104232800-104235400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr12:104233000-104235800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:104233000-104236000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:104233400-104234400	Flanking Active TSS	Fetal Intestine Small	intestine
11	chr12:104233400-104234600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:104233400-104235400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr12:104233400-104236000	Active TSS	Fetal Brain Female	brain
14	chr12:104233600-104234400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:104233600-104234400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:104233600-104234400	Enhancers	Small Intestine	intestine
17	chr12:104233600-104234400	Enhancers	Stomach Mucosa	stomach
18	chr12:104233600-104234600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:104233600-104234600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr12:104233600-104234800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr12:104233600-104235600	Active TSS	HSMMtube	muscle
22	chr12:104233600-104235800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:104233600-104236000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr12:104233600-104236000	Active TSS	Brain Substantia Nigra	brain
25	chr12:104233800-104234400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr12:104233800-104234400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:104233800-104234400	Flanking Active TSS	Lung	lung
28	chr12:104233800-104234400	Flanking Active TSS	Psoas Muscle	Psoas
29	chr12:104233800-104234600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr12:104233800-104234600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr12:104233800-104234600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:104233800-104234600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr12:104233800-104234600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr12:104233800-104234600	Flanking Active TSS	Placenta	Placenta
35	chr12:104233800-104235400	Bivalent/Poised TSS	Fetal Stomach	stomach
36	chr12:104233800-104235400	Active TSS	NHLF	lung
37	chr12:104233800-104235800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:104233800-104235800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr12:104234000-104234400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:104234000-104234400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:104234000-104234400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr12:104234000-104234400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:104234000-104234400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr12:104234000-104234600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr12:104234000-104234600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:104234000-104234600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:104234000-104234600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:104234000-104234800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:104234000-104234800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr12:104234000-104234800	Flanking Bivalent TSS/Enh	Thymus	Thymus

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