Variant report

Variant	esv3359395
Chromosome Location	chr13:95954035-95954389
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	ARID3A	chr13:95954220-95954222	K562	blood:	n/a	n/a
2	ATF2	chr13:95953752-95954132	GM12878	blood:	n/a	n/a
3	BACH1	chr13:95953247-95954203	H1-hESC	embryonic stem cell:	n/a	n/a
4	BCLAF1	chr13:95953476-95954069	GM12878	blood:	n/a	chr13:95953785-95953794 chr13:95953720-95953733 chr13:95953620-95953633
5	BHLHE40	chr13:95953022-95954602	GM12878	blood:	n/a	chr13:95953784-95953800 chr13:95953446-95953462 chr13:95953443-95953459
6	BHLHE40	chr13:95954115-95954309	A549	lung:	n/a	n/a
7	BHLHE40	chr13:95953400-95954315	HepG2	liver:	n/a	chr13:95953784-95953800 chr13:95953446-95953462 chr13:95953443-95953459
8	BHLHE40	chr13:95953007-95954599	K562	blood:	n/a	chr13:95953784-95953800 chr13:95953446-95953462 chr13:95953443-95953459
9	CBX3	chr13:95953672-95954674	K562	blood:	n/a	n/a
10	CCNT2	chr13:95952980-95954262	K562	blood:	n/a	n/a
11	CEBPB	chr13:95953921-95954228	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr13:95954091-95954583	GM12878	blood:	n/a	n/a
13	CHD1	chr13:95952300-95954946	IMR90	lung:	n/a	chr13:95954182-95954189 chr13:95953205-95953215 chr13:95953384-95953394
14	CHD2	chr13:95954119-95954327	K562	blood:	n/a	chr13:95954182-95954189
15	CHD2	chr13:95952867-95954239	GM12878	blood:	n/a	chr13:95954182-95954189 chr13:95953205-95953215 chr13:95953384-95953394
16	CHD2	chr13:95953456-95954580	H1-hESC	embryonic stem cell:	n/a	chr13:95954182-95954189
17	CHD2	chr13:95952921-95954283	Hela-S3	cervix:	n/a	chr13:95954182-95954189 chr13:95953205-95953215 chr13:95953384-95953394
18	CREB1	chr13:95953512-95954150	HepG2	liver:	n/a	n/a
19	CREB1	chr13:95953642-95954621	H1-hESC	embryonic stem cell:	n/a	n/a
20	CREB1	chr13:95953570-95954182	K562	blood:	n/a	n/a
21	CREB1	chr13:95953148-95954330	A549	lung:	n/a	n/a
22	CREB1	chr13:95953362-95954176	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr13:95954320-95954470	WERI-Rb-1	eye:	n/a	n/a
24	CTCF	chr13:95954120-95954270	AG09309	skin:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
25	CTCF	chr13:95954300-95954450	HFF	foreskin:	n/a	n/a
26	CTCF	chr13:95954140-95954290	HMEC	breast:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
27	CTCF	chr13:95954140-95954290	AG10803	skin:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
28	CTCF	chr13:95954340-95954490	HEK293	kidney:	n/a	n/a
29	CTCF	chr13:95953561-95954051	K562	blood:	n/a	chr13:95953788-95953801
30	CTCF	chr13:95954380-95954530	NHDF-neo	bronchial:	n/a	n/a
31	CTCF	chr13:95954164-95954166	GM19238	blood:	n/a	n/a
32	CTCF	chr13:95954120-95954270	HEK293	kidney:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
33	CTCF	chr13:95954100-95954250	HVMF	connective:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
34	CTCF	chr13:95953940-95954090	GM12871	blood:	n/a	n/a
35	CTCF	chr13:95954060-95954210	HCM	heart:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
36	CTCF	chr13:95954120-95954270	HPAF	blood vessel:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
37	CTCF	chr13:95954240-95954390	RPTEC	kidney:	n/a	n/a
38	CTCF	chr13:95954380-95954530	GM12873	blood:	n/a	n/a
39	CTCF	chr13:95954060-95954210	GM12864	blood:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
40	CTCF	chr13:95954240-95954390	GM12865	blood:	n/a	n/a
41	CTCF	chr13:95954160-95954310	BE2_C	brain:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
42	CTCF	chr13:95954040-95954190	HFF	foreskin:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
43	CTCF	chr13:95954260-95954410	HAc	cerebellar:	n/a	n/a
44	CTCF	chr13:95954140-95954290	HCPEpiC	choroid plexus:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
45	CTCF	chr13:95954120-95954270	AG10803	skin:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
46	CTCF	chr13:95954160-95954310	GM12872	blood:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
47	CTCF	chr13:95954320-95954470	AoAF	blood vessel:	n/a	n/a
48	CTCF	chr13:95953980-95954130	GM12867	blood:	n/a	n/a
49	CTCF	chr13:95954120-95954270	AoAF	blood vessel:	n/a	chr13:95954171-95954184 chr13:95954172-95954182
50	CTCF	chr13:95952950-95954368	GM12878	blood:	n/a	chr13:95954171-95954184 chr13:95953788-95953801 chr13:95954172-95954182 chr13:95953090-95953103

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:95954382-95954432	Hela-S3	cervix:	n/a
2	chr13:95954382-95954432	Hela-S3	cervix:	n/a
3	chr13:95954382-95954432	NH-A	brain:	n/a
4	chr13:95954080-95954130	K562	blood:	n/a
5	chr13:95954382-95954432	AG09319	gingival:	n/a
6	chr13:95954080-95954130	MCF-7	breast:	n/a
7	chr13:95954382-95954432	NT2-D1	testis:	n/a
8	chr13:95954382-95954432	HCF	heart:	n/a
9	chr13:95954382-95954432	HPAEpiC	pulmonary alveolar:	n/a
10	chr13:95954382-95954432	Hepatocyte	liver:	n/a
11	chr13:95954080-95954130	H1-hESC	embryonic stem cell:	embryo
12	chr13:95954382-95954432	LNCaP	prostate:	n/a
13	chr13:95954080-95954130	HRPEpiC	eye:	n/a
14	chr13:95954382-95954432	SKMC	muscle:	n/a
15	chr13:95954382-95954432	HEEpiC	esophagus:	n/a
16	chr13:95954382-95954432	NHBE	bronchial:	n/a
17	chr13:95954080-95954130	A549	lung:	n/a
18	chr13:95954080-95954130	HEK293	kidney:	embryo
19	chr13:95954382-95954432	GM12878	blood:	n/a
20	chr13:95954080-95954130	PANC-1	pancreas:	n/a
21	chr13:95954382-95954432	MCF-7	breast:	n/a
22	chr13:95954080-95954130	HEEpiC	esophagus:	n/a
23	chr13:95954382-95954432	HAEpiC	amniotic membrane:	n/a
24	chr13:95954382-95954432	ovcar-3	ovarian:	n/a
25	chr13:95954382-95954432	RPTEC	kidney:	n/a
26	chr13:95954382-95954432	HCM	heart:	n/a
27	chr13:95954382-95954432	AG04450	lung:	fetal
28	chr13:95954080-95954130	GM06990	blood:	n/a
29	chr13:95954382-95954432	NB4	blood:	n/a
30	chr13:95954382-95954432	GM06990	blood:	n/a
31	chr13:95954080-95954130	PFSK-1	brain:	n/a
32	chr13:95954080-95954130	HNPCEpiC	eye:	n/a
33	chr13:95954382-95954432	AoSMC	blood vessel:	n/a
34	chr13:95954080-95954130	HIPEpiC	eye:	n/a
35	chr13:95954382-95954432	Caco-2	colon:	n/a
36	chr13:95954382-95954432	BE2_C	brain:	n/a
37	chr13:95954080-95954130	HepG2	liver:	n/a
38	chr13:95954080-95954130	GM19239	blood:	n/a
39	chr13:95954382-95954432	GM19239	blood:	n/a
40	chr13:95954080-95954130	SAEC	small airway:	n/a
41	chr13:95954382-95954432	GM12892	blood:	n/a
42	chr13:95954382-95954432	ECC-1	luminal epithelium:	n/a
43	chr13:95954382-95954432	AG10803	skin:	n/a
44	chr13:95954382-95954432	HNPCEpiC	eye:	n/a
45	chr13:95954382-95954432	ProgFib	skin:	n/a
46	chr13:95954080-95954130	U87	brain:	n/a
47	chr13:95954382-95954432	HepG2	liver:	n/a
48	chr13:95954080-95954130	BE2_C	brain:	n/a
49	chr13:95954382-95954432	K562	blood:	n/a
50	chr13:95954382-95954432	HRE	kidney:	n/a

Variant related genes	Relation type
ABCC4	TF binding region
ABCC4	CpG island

Extended variants
information (count: 16 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs574125287	chr13:95954039-95954040	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs540111395	chr13:95954066-95954067	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs182890365	chr13:95954093-95954094	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
4	rs576590975	chr13:95954171-95954172	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs545979280	chr13:95954177-95954178	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs562586143	chr13:95954201-95954202	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs869951	chr13:95954210-95954211	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs544412228	chr13:95954211-95954212	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs561244413	chr13:95954232-95954233	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs138925747	chr13:95954254-95954255	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs188838261	chr13:95954299-95954300	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs528306061	chr13:95954303-95954304	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs532741731	chr13:95954321-95954322	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs3814270	chr13:95954327-95954328	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs111643536	chr13:95954374-95954375	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs574786687	chr13:95954385-95954386	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Burkitt''s lymphoma	18698080	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Myoepithelioma	18604193	CNVD
Breast cancer	17133270	CNVD
Prostate cancer	18632612	CNVD
Melanoma	18172304	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Basal cell lymphoma	17053054	CNVD
Metanephric adenoma	20802469	CNVD
Gastric cancer	17908304	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Liposarcoma	21253554	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal cancer	21851588	CNVD
Omodysplasia	19481194	CNVD
Breast cancer	22032731	CNVD
Rhabdomyosarcoma	17210683	CNVD
Burkitt''s lymphoma	19759907	CNVD
Wilms tumour	21544195	CNVD
Developmental delay	21147756	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21183584	CNVD
Breast cancer	17603634	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thyroid cancer	19087340	CNVD
abortions and stillbirths	19751515	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute myeloid leukemia	19651601	CNVD
Congenital anomalies of the kidney and urinary tract	20467480	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Intellectual disability	22102821	CNVD

Chromatin state (count:164 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95950600-95954400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:95952000-95954600	Active TSS	A549	lung
3	chr13:95952200-95954200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:95952400-95954200	Active TSS	Brain Substantia Nigra	brain
5	chr13:95952400-95954200	Active TSS	Rectal Smooth Muscle	rectum
6	chr13:95952400-95954200	Active TSS	HSMM	muscle
7	chr13:95952400-95954400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:95952400-95954400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:95952400-95954400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:95952400-95954400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr13:95952400-95954400	Active TSS	NHDF-Ad	bronchial
12	chr13:95952400-95954600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:95952400-95954800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:95952400-95954800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:95952600-95954200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr13:95952600-95954200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr13:95952600-95954200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr13:95952600-95954200	Active TSS	Brain Cingulate Gyrus	brain
19	chr13:95952600-95954400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr13:95952600-95954400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr13:95952600-95954400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:95952600-95954400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr13:95952600-95954400	Active TSS	Psoas Muscle	Psoas
24	chr13:95952600-95954400	Active TSS	HSMMtube	muscle
25	chr13:95952600-95954600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr13:95952600-95954600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr13:95952600-95954600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr13:95952600-95954600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr13:95952600-95954600	Active TSS	Brain Anterior Caudate	brain
30	chr13:95952600-95954600	Active TSS	Brain Hippocampus Middle	brain
31	chr13:95952600-95954600	Active TSS	Fetal Brain Female	brain
32	chr13:95952600-95954600	Active TSS	Fetal Lung	lung
33	chr13:95952800-95954200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr13:95952800-95954200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:95952800-95954200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr13:95952800-95954200	Active TSS	Colon Smooth Muscle	Colon
37	chr13:95952800-95954400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:95952800-95954400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:95952800-95954400	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr13:95952800-95954400	Active TSS	Aorta	Aorta
41	chr13:95952800-95954400	Active TSS	Fetal Heart	heart
42	chr13:95952800-95954400	Active TSS	Ovary	ovary
43	chr13:95952800-95954400	Active TSS	NHLF	lung
44	chr13:95952800-95954800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr13:95953000-95954200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr13:95953000-95954200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr13:95953000-95954200	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr13:95953000-95954200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr13:95953000-95954200	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr13:95953000-95954200	Active TSS	Fetal Intestine Small	intestine

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