Variant report

Variant	esv3353715
Chromosome Location	chr19:41100494-41100719
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:119)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:119 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr19:41100048-41101329	A549	lung:	n/a	chr19:41100339-41100348 chr19:41100781-41100790
2	BHLHE40	chr19:41100522-41100575	K562	blood:	n/a	n/a
3	CEBPB	chr19:41100273-41100874	IMR90	lung:	n/a	n/a
4	CREB1	chr19:41100519-41101149	A549	lung:	n/a	n/a
5	CTCF	chr19:41100620-41100770	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr19:41100620-41100770	AG09319	gingival:	n/a	n/a
7	CTCF	chr19:41100620-41100770	HA-sp	spinal cord:	n/a	n/a
8	CTCF	chr19:41100600-41100750	HA-sp	spinal cord:	n/a	n/a
9	CTCF	chr19:41100640-41100790	AG04449	skin:	n/a	n/a
10	CTCF	chr19:41100596-41100919	K562	blood:	n/a	n/a
11	CTCF	chr19:41100440-41100590	AG10803	skin:	n/a	n/a
12	CTCF	chr19:41100640-41100790	HEK293	kidney:	n/a	n/a
13	CTCF	chr19:41100647-41100798	MCF-7	breast:	n/a	n/a
14	CTCF	chr19:41100660-41100810	HPAF	blood vessel:	n/a	n/a
15	CTCF	chr19:41100680-41100830	HCT-116	colon:	n/a	n/a
16	CTCF	chr19:41100622-41100780	ProgFib	skin:	n/a	n/a
17	CTCF	chr19:41100660-41100810	HMEC	breast:	n/a	n/a
18	CTCF	chr19:41100660-41100810	HRE	kidney:	n/a	n/a
19	CTCF	chr19:41100621-41100811	NHEK	skin:	n/a	n/a
20	CTCF	chr19:41100640-41100790	SAEC	small airway:	n/a	n/a
21	CTCF	chr19:41100580-41100730	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr19:41100640-41100795	MCF-7	breast:	n/a	n/a
23	CTCF	chr19:41100600-41100750	HEEpiC	esophagus:	n/a	n/a
24	CTCF	chr19:41100660-41100810	HBMEC	blood vessel:	n/a	n/a
25	CTCF	chr19:41100656-41100793	MCF-7	breast:	n/a	n/a
26	CTCF	chr19:41100598-41100826	Gliobla	brain:	n/a	n/a
27	CTCF	chr19:41100600-41100750	AG10803	skin:	n/a	n/a
28	CTCF	chr19:41100630-41100819	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr19:41100617-41100821	MCF-7	breast:	n/a	n/a
30	CTCF	chr19:41100620-41100770	HCPEpiC	choroid plexus:	n/a	n/a
31	CTCF	chr19:41100640-41100790	HMEC	breast:	n/a	n/a
32	CTCF	chr19:41100620-41100770	HCFaa	heart:	n/a	n/a
33	CTCF	chr19:41100576-41100824	IMR90	lung:	n/a	n/a
34	CTCF	chr19:41100700-41100850	RPTEC	kidney:	n/a	n/a
35	CTCF	chr19:41100620-41100770	HPAF	blood vessel:	n/a	n/a
36	CTCF	chr19:41100640-41100790	HAc	cerebellar:	n/a	n/a
37	CTCF	chr19:41100380-41100530	HPF	lung:	n/a	n/a
38	CTCF	chr19:41100380-41100530	HVMF	connective:	n/a	n/a
39	CTCF	chr19:41100580-41100730	BJ	skin:	n/a	n/a
40	CTCF	chr19:41100600-41100750	BE2_C	brain:	n/a	n/a
41	CTCF	chr19:41100597-41100884	K562	blood:	n/a	n/a
42	CTCF	chr19:41100600-41100750	MCF-7	breast:	n/a	n/a
43	CTCF	chr19:41100622-41100799	K562	blood:	n/a	n/a
44	CTCF	chr19:41100600-41100750	A549	lung:	n/a	n/a
45	CTCF	chr19:41100640-41100790	HMF	breast:	n/a	n/a
46	CTCF	chr19:41100660-41100810	BJ	skin:	n/a	n/a
47	CTCF	chr19:41100620-41100770	AG09309	skin:	n/a	n/a
48	CTCF	chr19:41100635-41100803	A549	lung:	n/a	n/a
49	CTCF	chr19:41100640-41100790	RPTEC	kidney:	n/a	n/a
50	CTCF	chr19:41100520-41100670	HRPEpiC	eye:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:40948223..40951399-chr19:41100513..41104736,3	MCF-7	breast:
2	chr19:41087979..41091275-chr19:41098562..41102111,3	MCF-7	breast:
3	chr19:41093850..41097927-chr19:41099715..41103880,5	K562	blood:

No data

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000167565	chromatin interactions
ENSG00000268366	chromatin interactions
ENSG00000160410	chromatin interactions

Extended variants
information (count: 8 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553115310	chr19:41100499-41100500	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs555907287	chr19:41100503-41100504	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs573703864	chr19:41100518-41100519	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs537939933	chr19:41100524-41100525	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs545523684	chr19:41100575-41100576	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs555752127	chr19:41100620-41100621	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs35669602	chr19:41100624-41100625	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs544916455	chr19:41100631-41100632	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Genital abnormality	22378287	CNVD
Hypospadia	22378287	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Astrocytoma	22246337	CNVD
Anaplastic thyroid cancer	18753363	CNVD

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
2	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
3	chr19:41086800-41100600	Weak transcription	Brain Angular Gyrus	brain
4	chr19:41087600-41102600	Weak transcription	Small Intestine	intestine
5	chr19:41094400-41102400	Weak transcription	Fetal Lung	lung
6	chr19:41094600-41101200	Weak transcription	Primary B cells from cord blood	blood
7	chr19:41094600-41102800	Weak transcription	Aorta	Aorta
8	chr19:41094600-41102800	Weak transcription	Left Ventricle	heart
9	chr19:41094800-41100600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:41094800-41100600	Weak transcription	HSMM	muscle
11	chr19:41095200-41100600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr19:41095200-41101000	Weak transcription	NHEK	skin
13	chr19:41095200-41102400	Weak transcription	HUVEC	blood vessel
14	chr19:41095200-41103200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:41097000-41100600	Weak transcription	Esophagus	oesophagus
16	chr19:41097000-41100600	Weak transcription	Pancreas	Pancrea
17	chr19:41097000-41102600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:41097000-41102600	Weak transcription	Right Ventricle	heart
19	chr19:41097200-41100600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:41097200-41100600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:41097200-41100600	Weak transcription	Gastric	stomach
22	chr19:41097400-41100600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:41097400-41100600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:41097400-41100600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:41097400-41102600	Weak transcription	Lung	lung
26	chr19:41097400-41102800	Weak transcription	Ovary	ovary
27	chr19:41097400-41102800	Weak transcription	Spleen	Spleen
28	chr19:41097600-41100800	Weak transcription	Thymus	Thymus
29	chr19:41097800-41100600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:41099800-41100600	Enhancers	Fetal Thymus	thymus
31	chr19:41099800-41101000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:41099800-41101200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr19:41100000-41101000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:41100000-41101000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr19:41100000-41101000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:41100000-41101000	Active TSS	Fetal Brain Female	brain
37	chr19:41100000-41101200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:41100200-41100600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:41100200-41100600	Enhancers	Osteobl	bone
40	chr19:41100200-41100800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:41100200-41100800	Weak transcription	Fetal Heart	heart
42	chr19:41100200-41101000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr19:41100200-41101000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr19:41100200-41101000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr19:41100200-41101000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr19:41100200-41101000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:41100200-41101200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr19:41100200-41101200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:41100200-41101200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:41100200-41101200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast

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