Variant report

Variant	esv3386118
Chromosome Location	chr4:645418-645598
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr4:645281-645660	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:645185-645583	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:645141-645436	ECC-1	luminal epithelium:	n/a	n/a
4	TBP	chr4:645404-645509	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr4:645066-645588	ECC-1	luminal epithelium:	n/a	n/a
6	ZNF143	chr4:645421-645592	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:645551-645601	IMR90	lung:	fetal
2	chr4:645440-645490	PFSK-1	brain:	n/a
3	chr4:645551-645601	U87	brain:	n/a
4	chr4:645440-645490	SK-N-SH_RA	brain:	n/a
5	chr4:645440-645490	RPTEC	kidney:	n/a
6	chr4:645551-645601	HEK293	kidney:	embryo
7	chr4:645551-645601	Caco-2	colon:	n/a
8	chr4:645440-645490	AG04449	skin:	fetal
9	chr4:645440-645490	PrEC	prostate:	n/a
10	chr4:645551-645601	Jurkat	blood:	n/a
11	chr4:645440-645490	Jurkat	blood:	n/a
12	chr4:645440-645490	MCF10A-Er-Src	breast:	n/a
13	chr4:645551-645601	SKMC	muscle:	n/a
14	chr4:645551-645601	NT2-D1	testis:	n/a
15	chr4:645551-645601	CMK	blood:	n/a
16	chr4:645551-645601	NHBE	bronchial:	n/a
17	chr4:645551-645601	AG04449	skin:	fetal
18	chr4:645551-645601	MCF10A-Er-Src	breast:	n/a
19	chr4:645551-645601	HL-60	blood:	n/a
20	chr4:645551-645601	PFSK-1	brain:	n/a
21	chr4:645440-645490	SK-N-MC	brain:	n/a
22	chr4:645440-645490	PANC-1	pancreas:	n/a
23	chr4:645440-645490	NH-A	brain:	n/a
24	chr4:645440-645490	HepG2	liver:	n/a
25	chr4:645551-645601	HNPCEpiC	eye:	n/a
26	chr4:645551-645601	HRCEpiC	kidney:	n/a
27	chr4:645440-645490	T-47D	breast:	n/a
28	chr4:645440-645490	BJ	skin:	n/a
29	chr4:645551-645601	LNCaP	prostate:	n/a
30	chr4:645551-645601	HEEpiC	esophagus:	n/a
31	chr4:645440-645490	ovcar-3	ovarian:	n/a
32	chr4:645440-645490	IMR90	lung:	fetal
33	chr4:645551-645601	AG09309	skin:	n/a
34	chr4:645551-645601	AoSMC	blood vessel:	n/a
35	chr4:645440-645490	CMK	blood:	n/a
36	chr4:645551-645601	HCT-116	colon:	n/a
37	chr4:645551-645601	BE2_C	brain:	n/a
38	chr4:645551-645601	HRE	kidney:	n/a
39	chr4:645551-645601	H1-hESC	embryonic stem cell:	embryo
40	chr4:645440-645490	SKMC	muscle:	n/a
41	chr4:645440-645490	Hepatocyte	liver:	n/a
42	chr4:645551-645601	HCPEpiC	choroid plexus:	n/a
43	chr4:645440-645490	AG09319	gingival:	n/a
44	chr4:645551-645601	PANC-1	pancreas:	n/a
45	chr4:645440-645490	HCM	heart:	n/a
46	chr4:645440-645490	LNCaP	prostate:	n/a
47	chr4:645551-645601	HMEC	breast:	n/a
48	chr4:645551-645601	SK-N-SH	brain:	n/a
49	chr4:645440-645490	U87	brain:	n/a
50	chr4:645440-645490	HPAEpiC	pulmonary alveolar:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:
2	chr4:644808..646339-chr4:648173..650037,2	K562	blood:
3	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:

No data

Variant related genes	Relation type
PDE6B	TF binding region
PDE6B	CpG island
ENSG00000242686	chromatin interactions
ENSG00000133256	chromatin interactions

Extended variants
information (count: 25 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546509994	chr4:645423-645424	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs571123099	chr4:645437-645438	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs532245300	chr4:645441-645442	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs550463030	chr4:645443-645444	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs568473241	chr4:645444-645445	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs535908282	chr4:645446-645447	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs554628124	chr4:645454-645455	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs566479743	chr4:645459-645460	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs533904955	chr4:645477-645478	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs553577434	chr4:645479-645480	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs578222126	chr4:645482-645483	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs13143260	chr4:645489-645490	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs13143262	chr4:645490-645491	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs547855534	chr4:645495-645496	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs575708533	chr4:645496-645497	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs542681483	chr4:645508-645509	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs13133489	chr4:645512-645513	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs528540285	chr4:645516-645517	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs540741337	chr4:645519-645520	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs13143415	chr4:645522-645523	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs532184805	chr4:645525-645526	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs71602491	chr4:645526-645527	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs28520978	chr4:645548-645549	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs71602492	chr4:645568-645569	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs369165515	chr4:645594-645595	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pancreatic cancer	17952125	CNVD
Type 2 diabetes	21754918	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21509527	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:640400-648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:643000-646000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:643200-646200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr4:643200-648200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:644400-646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:644600-645800	Enhancers	Gastric	stomach
13	chr4:644600-646200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:644800-645800	Enhancers	Pancreas	Pancrea
15	chr4:645000-645600	Active TSS	Brain Anterior Caudate	brain
16	chr4:645000-645600	Bivalent/Poised TSS	HepG2	liver
17	chr4:645000-646000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:645000-648200	Weak transcription	Esophagus	oesophagus
19	chr4:645200-645600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:645200-645800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:645200-646600	Active TSS	Brain Substantia Nigra	brain
22	chr4:645400-645600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
23	chr4:645400-645600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:645400-645600	Active TSS	Brain Cingulate Gyrus	brain
25	chr4:645400-645600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr4:645400-645600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr4:645400-645600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr4:645400-645800	Weak transcription	Brain Angular Gyrus	brain

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