Variant report

Variant	rs112089462
Chromosome Location	chr20:24449695-24449696
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	SIN3A	chr20:24449529-24452302	H1-hESC	embryonic stem cell:	n/a	chr20:24450622-24450635 chr20:24449957-24449970
2	SP1	chr20:24449560-24449989	H1-hESC	embryonic stem cell:	n/a	chr20:24449799-24449811 chr20:24449801-24449810 chr20:24449800-24449809 chr20:24449799-24449811 chr20:24449800-24449810 chr20:24449941-24449955 chr20:24449799-24449810 chr20:24449800-24449814
3	TEAD4	chr20:24449515-24450031	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr20:24449550-24450038	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr20:24449519-24449987	H1-hESC	embryonic stem cell:	n/a	chr20:24449962-24449976 chr20:24449710-24449724 chr20:24449801-24449810
6	POLR2A	chr20:24449547-24450560	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAFK	chr20:24449634-24449799	H1-hESC	embryonic stem cell:	n/a	n/a
8	EGR1	chr20:24449494-24449951	H1-hESC	embryonic stem cell:	n/a	chr20:24449800-24449810
9	TAF1	chr20:24449614-24449877	H1-hESC	embryonic stem cell:	n/a	n/a
10	KAP1	chr20:24449559-24450130	HEK293	kidney:	n/a	n/a
11	TEAD4	chr20:24449577-24449996	ECC-1	luminal epithelium:	n/a	n/a
12	CHD2	chr20:24449687-24449904	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOSL1	chr20:24449506-24449961	H1-hESC	embryonic stem cell:	n/a	n/a
14	CEBPB	chr20:24449689-24449861	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr20:24449652-24449992	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF263	chr20:24449678-24451203	HEK293-T-REx	kidney:	n/a	chr20:24449948-24449957 chr20:24449934-24449955
17	FOSL1	chr20:24449505-24449961	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF143	chr20:24449178-24450293	H1-hESC	embryonic stem cell:	n/a	chr20:24450087-24450105 chr20:24449963-24449973 chr20:24449299-24449318
19	TBP	chr20:24449648-24450662	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr20:24449660-24449810	MCF-7	breast:	n/a	chr20:24449751-24449759
21	SIN3AK20	chr20:24449666-24449974	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTBP2	chr20:24449619-24450490	H1-hESC	embryonic stem cell:	n/a	n/a
23	TCF12	chr20:24449651-24449949	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr20:24449604-24449867	H1-hESC	embryonic stem cell:	n/a	chr20:24449710-24449724 chr20:24449801-24449810
25	RAD21	chr20:24449481-24450052	H1-hESC	embryonic stem cell:	n/a	chr20:24449975-24449989 chr20:24449803-24449813
26	HDAC2	chr20:24449680-24450015	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:24449668-24449718	AoSMC	blood vessel:	n/a
2	chr20:24449668-24449718	Hepatocyte	liver:	n/a
3	chr20:24449668-24449718	Caco-2	colon:	n/a
4	chr20:24449668-24449718	HNPCEpiC	eye:	n/a
5	chr20:24449668-24449718	SKMC	muscle:	n/a
6	chr20:24449668-24449718	HCT-116	colon:	n/a
7	chr20:24449668-24449718	HMEC	breast:	n/a
8	chr20:24449668-24449718	U87	brain:	n/a
9	chr20:24449668-24449718	ProgFib	skin:	n/a
10	chr20:24449668-24449718	NT2-D1	testis:	n/a
11	chr20:24449668-24449718	HCF	heart:	n/a
12	chr20:24449668-24449718	HEK293	kidney:	embryo
13	chr20:24449668-24449718	HPAEpiC	pulmonary alveolar:	n/a
14	chr20:24449668-24449718	K562	blood:	n/a
15	chr20:24449668-24449718	NB4	blood:	n/a
16	chr20:24449668-24449718	PANC-1	pancreas:	n/a
17	chr20:24449668-24449718	Hela-S3	cervix:	n/a
18	chr20:24449668-24449718	IMR90	lung:	fetal
19	chr20:24449668-24449718	SAEC	small airway:	n/a
20	chr20:24449668-24449718	NHBE	bronchial:	n/a
21	chr20:24449668-24449718	HRE	kidney:	n/a
22	chr20:24449668-24449718	SK-N-MC	brain:	n/a
23	chr20:24449668-24449718	GM19239	blood:	n/a
24	chr20:24449668-24449718	HIPEpiC	eye:	n/a
25	chr20:24449668-24449718	ovcar-3	ovarian:	n/a
26	chr20:24449668-24449718	AG04449	skin:	fetal
27	chr20:24449668-24449718	GM12892	blood:	n/a
28	chr20:24449668-24449718	AG10803	skin:	n/a
29	chr20:24449668-24449718	SK-N-SH_RA	brain:	n/a
30	chr20:24449668-24449718	HL-60	blood:	n/a
31	chr20:24449668-24449718	T-47D	breast:	n/a
32	chr20:24449668-24449718	ECC-1	luminal epithelium:	n/a
33	chr20:24449668-24449718	HRCEpiC	kidney:	n/a
34	chr20:24449668-24449718	SK-N-SH	brain:	n/a
35	chr20:24449668-24449718	BE2_C	brain:	n/a
36	chr20:24449668-24449718	HEEpiC	esophagus:	n/a
37	chr20:24449668-24449718	LNCaP	prostate:	n/a
38	chr20:24449668-24449718	AG09309	skin:	n/a
39	chr20:24449668-24449718	PFSK-1	brain:	n/a
40	chr20:24449668-24449718	HRPEpiC	eye:	n/a
41	chr20:24449668-24449718	AG04450	lung:	fetal
42	chr20:24449668-24449718	A549	lung:	n/a
43	chr20:24449668-24449718	HepG2	liver:	n/a
44	chr20:24449668-24449718	HAEpiC	amniotic membrane:	n/a
45	chr20:24449668-24449718	GM06990	blood:	n/a
46	chr20:24449668-24449718	GM12891	blood:	n/a
47	chr20:24449668-24449718	Jurkat	blood:	n/a
48	chr20:24449668-24449718	BJ	skin:	n/a
49	chr20:24449668-24449718	HCPEpiC	choroid plexus:	n/a
50	chr20:24449668-24449718	NHDF-neo	bronchial:	n/a

Variant related genes	Relation type
SYNDIG1	TF binding region
SYNDIG1	CpG island

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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv833946	chr20:24320375-24490702	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3400513	chr20:24449177-24451725	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24439800-24449800	Weak transcription	Right Atrium	heart
2	chr20:24446000-24449800	Weak transcription	Aorta	Aorta
3	chr20:24448000-24450000	Bivalent Enhancer	Fetal Thymus	thymus
4	chr20:24449000-24449800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
5	chr20:24449000-24449800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:24449000-24449800	Enhancers	Fetal Heart	heart
7	chr20:24449200-24451200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:24449200-24452200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr20:24449400-24449800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr20:24449400-24449800	Flanking Active TSS	Fetal Brain Female	brain
11	chr20:24449400-24449800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
12	chr20:24449400-24449800	Weak transcription	Gastric	stomach
13	chr20:24449400-24449800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
14	chr20:24449400-24450000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
15	chr20:24449400-24450000	Enhancers	Fetal Brain Male	brain
16	chr20:24449400-24450000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
17	chr20:24449400-24450400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr20:24449400-24451000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr20:24449400-24451000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr20:24449400-24451000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr20:24449400-24451600	Bivalent/Poised TSS	Colonic Mucosa	Colon
22	chr20:24449400-24452200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr20:24449400-24452200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr20:24449400-24452200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr20:24449400-24452200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:24449400-24452200	Active TSS	Brain Angular Gyrus	brain
27	chr20:24449400-24452200	Active TSS	Brain Cingulate Gyrus	brain
28	chr20:24449400-24452400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr20:24449400-24452400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr20:24449400-24452400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr20:24449600-24449800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr20:24449600-24449800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr20:24449600-24449800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr20:24449600-24449800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
35	chr20:24449600-24449800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:24449600-24449800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr20:24449600-24449800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
38	chr20:24449600-24449800	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr20:24449600-24449800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr20:24449600-24449800	Bivalent/Poised TSS	Fetal Kidney	kidney
41	chr20:24449600-24449800	Bivalent Enhancer	Placenta	Placenta
42	chr20:24449600-24449800	Enhancers	Left Ventricle	heart
43	chr20:24449600-24449800	Flanking Active TSS	Right Ventricle	heart
44	chr20:24449600-24449800	Bivalent Enhancer	Thymus	Thymus
45	chr20:24449600-24449800	Flanking Active TSS	NH-A	brain
46	chr20:24449600-24450000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr20:24449600-24450000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr20:24449600-24450000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
49	chr20:24449600-24450000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
50	chr20:24449600-24450000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain

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