Variant report

Variant	esv1062103
Chromosome Location	chr19:52192150-52192160
allele	n/a
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	ATF3	chr19:52191900-52192528	A549	lung:	n/a	n/a
2	ATF3	chr19:52191947-52192445	A549	lung:	n/a	n/a
3	BCL3	chr19:52191885-52194262	A549	lung:	n/a	chr19:52193326-52193335 chr19:52194168-52194181 chr19:52192591-52192604 chr19:52192366-52192379 chr19:52194169-52194178 chr19:52193878-52193887 chr19:52192370-52192383 chr19:52193169-52193182 chr19:52193321-52193334
4	BCL3	chr19:52191859-52192877	A549	lung:	n/a	chr19:52192591-52192604 chr19:52192366-52192379 chr19:52192370-52192383
5	BHLHE40	chr19:52191942-52192398	K562	blood:	n/a	n/a
6	CBX3	chr19:52191887-52192322	K562	blood:	n/a	n/a
7	CEBPB	chr19:52192093-52192424	H1-hESC	embryonic stem cell:	n/a	n/a
8	CHD2	chr19:52192062-52192770	Hela-S3	cervix:	n/a	n/a
9	CHD2	chr19:52192156-52192420	H1-hESC	embryonic stem cell:	n/a	n/a
10	CREB1	chr19:52192065-52192529	A549	lung:	n/a	n/a
11	CTBP2	chr19:52191102-52195103	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr19:52192100-52192250	AG10803	skin:	n/a	n/a
13	CTCF	chr19:52192086-52192263	Lung_OC	lung:	n/a	n/a
14	CTCF	chr19:52192152-52192316	NHEK	skin:	n/a	n/a
15	CTCF	chr19:52192160-52192310	HMEC	breast:	n/a	n/a
16	CTCF	chr19:52192100-52192250	AG09319	gingival:	n/a	n/a
17	CTCF	chr19:52192126-52192303	Fibrobl	skin:	n/a	n/a
18	CTCF	chr19:52192119-52192287	ProgFib	skin:	n/a	n/a
19	CTCF	chr19:52192090-52192329	Kidney_OC	kidney:	n/a	n/a
20	CTCF	chr19:52192140-52192290	Caco-2	colon:	n/a	n/a
21	CTCF	chr19:52192100-52192250	BJ	skin:	n/a	n/a
22	E2F6	chr19:52190940-52192581	A549	lung:	n/a	chr19:52192365-52192375 chr19:52192370-52192379
23	EGR1	chr19:52191986-52192494	H1-hESC	embryonic stem cell:	n/a	chr19:52192372-52192382 chr19:52192426-52192436 chr19:52192369-52192379
24	EGR1	chr19:52192011-52192500	H1-hESC	embryonic stem cell:	n/a	chr19:52192372-52192382 chr19:52192426-52192436 chr19:52192369-52192379
25	ELF1	chr19:52192099-52192430	A549	lung:	n/a	n/a
26	EP300	chr19:52191908-52192466	K562	blood:	n/a	n/a
27	EP300	chr19:52192045-52192653	SK-N-SH_RA	brain:	n/a	chr19:52192452-52192468
28	EP300	chr19:52191930-52193491	SK-N-SH	brain:	n/a	chr19:52192452-52192468
29	EP300	chr19:52191959-52192948	ECC-1	luminal epithelium:	n/a	chr19:52192452-52192468
30	EP300	chr19:52191850-52192701	A549	lung:	n/a	chr19:52192452-52192468
31	EP300	chr19:52191504-52194723	A549	lung:	n/a	chr19:52192452-52192468
32	EP300	chr19:52191946-52192655	SK-N-SH_RA	brain:	n/a	chr19:52192452-52192468
33	ETS1	chr19:52191971-52192513	A549	lung:	n/a	chr19:52192370-52192381 chr19:52192430-52192443
34	ETS1	chr19:52192000-52192317	A549	lung:	n/a	n/a
35	FOSL2	chr19:52191061-52192493	A549	lung:	n/a	n/a
36	FOXP2	chr19:52192152-52192825	PFSK-1	brain:	n/a	n/a
37	GABPA	chr19:52191862-52192255	A549	lung:	n/a	n/a
38	GATA3	chr19:52191095-52192781	A549	lung:	n/a	chr19:52192029-52192037 chr19:52191852-52191862
39	GATA3	chr19:52191959-52194396	A549	lung:	n/a	chr19:52192029-52192037
40	HA-E2F1	chr19:52191488-52192498	MCF-7	breast:	n/a	chr19:52192365-52192375 chr19:52192370-52192379
41	HCFC1	chr19:52191888-52192731	Hela-S3	cervix:	n/a	n/a
42	HDAC2	chr19:52191912-52192197	K562	blood:	n/a	n/a
43	HDAC2	chr19:52192009-52192292	K562	blood:	n/a	n/a
44	HDAC2	chr19:52192009-52192530	MCF-7	breast:	n/a	n/a
45	HEY1	chr19:52192062-52192490	HepG2	liver:	n/a	n/a
46	HEY1	chr19:52192082-52192395	K562	blood:	n/a	n/a
47	IRF1	chr19:52191992-52192467	K562	blood:	n/a	n/a
48	JUND	chr19:52192072-52192776	K562	blood:	n/a	n/a
49	JUND	chr19:52191921-52192468	A549	lung:	n/a	n/a
50	JUND	chr19:52192024-52192316	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52190822..52192582-chr19:52204625..52207087,2	K562	blood:
2	chr19:52191148..52193451-chr19:52208033..52210074,2	MCF-7	breast:
3	chr19:52191310..52193737-chr19:54959271..54961784,2	MCF-7	breast:
4	chr19:51979609..51981467-chr19:52190733..52192569,2	K562	blood:
5	chr19:52189832..52192322-chr19:52204625..52207481,2	K562	blood:
6	chr19:52186234..52189243-chr19:52190984..52192960,3	K562	blood:
7	chr19:52192066..52193660-chr19:52283404..52285811,2	MCF-7	breast:
8	chr19:52166500..52170915-chr19:52189684..52193816,5	MCF-7	breast:
9	chr19:52171940..52173838-chr19:52191282..52193363,2	MCF-7	breast:
10	chr19:52191800..52194773-chr19:52195976..52198030,3	K562	blood:
11	chr19:52190894..52195343-chr19:52204099..52207909,11	MCF-7	breast:
12	chr19:52191235..52193231-chr19:52302966..52304607,2	MCF-7	breast:
13	chr19:52191774..52192450-chr3:55003928..55004428,2	HCT-116	colon:
14	chr19:52189901..52192880-chr19:52273718..52275861,2	MCF-7	breast:
15	chr17:48943612..48944270-chr19:52191708..52192701,3	HCT-116	colon:
16	chr19:52191055..52194888-chr19:52301421..52305190,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HAS1-1	chr19:52190491-52192335	NONHSAT067461

Variant related genes	Relation type
MIR99B	TF binding region
MIRLET7E	TF binding region
MIR125A	TF binding region
SPACA6P	TF binding region
ENSG00000273318	TF binding region
ENSG00000269959	chromatin interactions
ENSG00000213822	chromatin interactions
ENSG00000229980	chromatin interactions
ENSG00000273318	chromatin interactions
ENSG00000182310	chromatin interactions
ENSG00000141232	chromatin interactions
ENSG00000167615	chromatin interactions
ENSG00000226696	chromatin interactions
ENSG00000198972	chromatin interactions
ENSG00000208008	chromatin interactions
ENSG00000238486	chromatin interactions

Extended variants
information (count: 4 )
Associated
traits (count: 66 )

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	rs71189610	chr19:52192150-52192151	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	15 gene(s)	Overlapped CNVs	n/a
2	rs139781159	chr19:52192151-52192152	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	15 gene(s)	Overlapped CNVs	n/a
3	rs374609043	chr19:52192155-52192156	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	15 gene(s)	Overlapped CNVs	n/a
4	rs138147326	chr19:52192156-52192157	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	15 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

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
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	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
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Adrenocortical carcinoma	18281524	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Cancer	20164920	CNVD
Melanoma	17363583	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Ovarian cancer	22355333	CNVD

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52190400-52194600	Active TSS	Fetal Brain Female	brain
2	chr19:52190600-52192200	Flanking Active TSS	HMEC	breast
3	chr19:52190800-52192200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:52190800-52192200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:52190800-52192200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr19:52190800-52192200	Flanking Active TSS	Fetal Heart	heart
7	chr19:52190800-52192200	Flanking Active TSS	Fetal Lung	lung
8	chr19:52190800-52192200	Flanking Active TSS	Placenta	Placenta
9	chr19:52190800-52192200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr19:52190800-52192200	Flanking Active TSS	Osteobl	bone
11	chr19:52190800-52194400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:52190800-52194400	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:52190800-52194800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:52190800-52194800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:52190800-52195000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr19:52190800-52195000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:52190800-52195200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr19:52191000-52192200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr19:52191000-52192200	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr19:52191000-52192200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr19:52191000-52192200	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr19:52191000-52192200	Flanking Active TSS	HUVEC	blood vessel
23	chr19:52191000-52193400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr19:52191000-52194000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr19:52191000-52194600	Active TSS	Psoas Muscle	Psoas
26	chr19:52191000-52194600	Active TSS	A549	lung
27	chr19:52191000-52195200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr19:52191000-52195400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr19:52191000-52195800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:52191200-52192400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:52191200-52193600	Active TSS	Hela-S3	cervix
32	chr19:52191200-52194800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:52191200-52194800	Active TSS	Left Ventricle	heart
34	chr19:52191200-52195000	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr19:52191200-52195000	Active TSS	Ovary	ovary
36	chr19:52191200-52196200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:52191200-52196200	Active TSS	Fetal Kidney	kidney
38	chr19:52191400-52192200	Flanking Active TSS	Colonic Mucosa	Colon
39	chr19:52191400-52192400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr19:52191400-52192400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:52191400-52192400	Bivalent/Poised TSS	HepG2	liver
42	chr19:52191400-52193400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
43	chr19:52191400-52194400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:52191400-52194600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:52191400-52194600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:52191400-52194600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:52191400-52194800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:52191400-52194800	Active TSS	Aorta	Aorta
49	chr19:52191400-52195000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr19:52191400-52195200	Active TSS	H1 Cell Line	embryonic stem cell

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