Variant report

Variant	esv17722
Chromosome Location	chr3:139653748-139654307
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:125)
CpG islands
(count:306)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:125 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr3:139654108-139654260	H1-hESC	embryonic stem cell:	n/a	n/a
2	CCNT2	chr3:139654009-139654199	K562	blood:	n/a	n/a
3	CHD2	chr3:139653445-139653754	H1-hESC	embryonic stem cell:	n/a	n/a
4	CREB1	chr3:139653808-139654178	A549	lung:	n/a	chr3:139653971-139653984
5	CREB1	chr3:139653000-139654183	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
6	CREB1	chr3:139653164-139654436	H1-hESC	embryonic stem cell:	n/a	chr3:139653971-139653984
7	CTBP2	chr3:139653274-139655142	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:139654064-139654274	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:139653917-139654434	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:139654260-139654410	WERI-Rb-1	eye:	n/a	n/a
11	CTCF	chr3:139654200-139654350	MCF-7	breast:	n/a	n/a
12	CTCF	chr3:139654200-139654350	HepG2	liver:	n/a	n/a
13	CTCF	chr3:139654018-139654020	MCF-7	breast:	n/a	n/a
14	CTCF	chr3:139654300-139654450	GM12869	blood:	n/a	n/a
15	CTCF	chr3:139654220-139654370	HA-sp	spinal cord:	n/a	n/a
16	CTCF	chr3:139654200-139654350	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr3:139654080-139654230	GM12869	blood:	n/a	n/a
18	CTCF	chr3:139654180-139654330	WERI-Rb-1	eye:	n/a	n/a
19	CTCF	chr3:139654100-139654250	GM12875	blood:	n/a	n/a
20	CTCF	chr3:139654092-139654263	Fibrobl	skin:	n/a	n/a
21	CTCF	chr3:139654128-139654228	GM12891	blood:	n/a	n/a
22	CTCF	chr3:139653978-139654452	MCF-7	breast:	n/a	n/a
23	CTCF	chr3:139654280-139654430	GM06990	blood:	n/a	n/a
24	CTCF	chr3:139654087-139654357	MCF-7	breast:	n/a	n/a
25	CTCF	chr3:139654160-139654310	AG04449	skin:	n/a	n/a
26	CTCF	chr3:139654156-139654258	Pancreas_OC	pancreas:	n/a	n/a
27	CTCF	chr3:139654080-139654230	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr3:139653397-139653844	MCF-7	breast:	n/a	n/a
29	CTCF	chr3:139654140-139654290	HBMEC	blood vessel:	n/a	n/a
30	CTCF	chr3:139654148-139654158	GM10266	blood:	n/a	n/a
31	CTCF	chr3:139653980-139654130	GM12871	blood:	n/a	n/a
32	CTCF	chr3:139654100-139654250	GM12865	blood:	n/a	n/a
33	CTCF	chr3:139654087-139654336	NHEK	skin:	n/a	n/a
34	CTCF	chr3:139654160-139654310	MCF-7	breast:	n/a	n/a
35	CTCF	chr3:139654152-139654155	Pancreas_OC	pancreas:	n/a	n/a
36	CTCF	chr3:139654180-139654330	BE2_C	brain:	n/a	n/a
37	CTCF	chr3:139654304-139654376	GM12891	blood:	n/a	n/a
38	CTCF	chr3:139654240-139654390	Caco-2	colon:	n/a	n/a
39	CTCF	chr3:139653220-139654254	A549	lung:	n/a	n/a
40	CTCF	chr3:139653316-139653757	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr3:139653888-139654376	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:139654120-139654270	AG04449	skin:	n/a	n/a
43	CTCF	chr3:139654080-139654230	HCPEpiC	choroid plexus:	n/a	n/a
44	CTCF	chr3:139654006-139654395	MCF-7	breast:	n/a	n/a
45	CTCF	chr3:139654136-139654143	A549	lung:	n/a	n/a
46	CTCF	chr3:139653312-139653837	MCF-7	breast:	n/a	n/a
47	CTCF	chr3:139654120-139654270	HMEC	breast:	n/a	n/a
48	CTCF	chr3:139654180-139654330	HEK293	kidney:	n/a	n/a
49	CTCF	chr3:139654060-139654210	GM12875	blood:	n/a	n/a
50	CTCF	chr3:139654146-139654201	A549	lung:	n/a	n/a

(count:306 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:139654264-139654314	SK-N-MC	brain:	n/a
2	chr3:139654264-139654314	SK-N-MC	brain:	n/a
3	chr3:139654245-139654295	RPTEC	kidney:	n/a
4	chr3:139653872-139653922	T-47D	breast:	n/a
5	chr3:139654245-139654295	AG10803	skin:	n/a
6	chr3:139654245-139654295	PANC-1	pancreas:	n/a
7	chr3:139654264-139654314	HCF	heart:	n/a
8	chr3:139653928-139653978	BJ	skin:	n/a
9	chr3:139654264-139654314	HCM	heart:	n/a
10	chr3:139653872-139653922	HNPCEpiC	eye:	n/a
11	chr3:139654245-139654295	HRCEpiC	kidney:	n/a
12	chr3:139653872-139653922	ECC-1	luminal epithelium:	n/a
13	chr3:139653928-139653978	NB4	blood:	n/a
14	chr3:139653915-139653965	HCM	heart:	n/a
15	chr3:139654264-139654314	Jurkat	blood:	n/a
16	chr3:139653915-139653965	HAEpiC	amniotic membrane:	n/a
17	chr3:139653928-139653978	A549	lung:	n/a
18	chr3:139653872-139653922	MCF-7	breast:	n/a
19	chr3:139653915-139653965	MCF-7	breast:	n/a
20	chr3:139654264-139654314	HepG2	liver:	n/a
21	chr3:139653915-139653965	H1-hESC	embryonic stem cell:	embryo
22	chr3:139654245-139654295	HEK293	kidney:	embryo
23	chr3:139653915-139653965	HRCEpiC	kidney:	n/a
24	chr3:139654245-139654295	A549	lung:	n/a
25	chr3:139653915-139653965	HRPEpiC	eye:	n/a
26	chr3:139653915-139653965	HL-60	blood:	n/a
27	chr3:139653928-139653978	HRPEpiC	eye:	n/a
28	chr3:139654264-139654314	SK-N-SH_RA	brain:	n/a
29	chr3:139654264-139654314	AG10803	skin:	n/a
30	chr3:139654264-139654314	HPAEpiC	pulmonary alveolar:	n/a
31	chr3:139653872-139653922	PANC-1	pancreas:	n/a
32	chr3:139653872-139653922	AoSMC	blood vessel:	n/a
33	chr3:139653872-139653922	HPAEpiC	pulmonary alveolar:	n/a
34	chr3:139653928-139653978	BE2_C	brain:	n/a
35	chr3:139654245-139654295	HCM	heart:	n/a
36	chr3:139653872-139653922	PrEC	prostate:	n/a
37	chr3:139654264-139654314	U87	brain:	n/a
38	chr3:139653928-139653978	Jurkat	blood:	n/a
39	chr3:139654264-139654314	SK-N-SH	brain:	n/a
40	chr3:139653928-139653978	ovcar-3	ovarian:	n/a
41	chr3:139653915-139653965	PANC-1	pancreas:	n/a
42	chr3:139654264-139654314	NHBE	bronchial:	n/a
43	chr3:139654264-139654314	HIPEpiC	eye:	n/a
44	chr3:139653928-139653978	SK-N-SH_RA	brain:	n/a
45	chr3:139654245-139654295	Caco-2	colon:	n/a
46	chr3:139653872-139653922	RPTEC	kidney:	n/a
47	chr3:139653928-139653978	GM19239	blood:	n/a
48	chr3:139653928-139653978	AG04449	skin:	fetal
49	chr3:139654245-139654295	HEEpiC	esophagus:	n/a
50	chr3:139653872-139653922	SAEC	small airway:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:139270922..139271855-chr3:139653137..139653973,3	MCF-7	breast:
2	chr3:139347937..139348556-chr3:139653424..139653964,2	MCF-7	breast:
3	chr3:139282929..139283874-chr3:139652757..139653752,4	MCF-7	breast:
4	chr3:139437070..139437910-chr3:139653098..139654016,8	MCF-7	breast:
5	chr3:139307203..139308238-chr3:139653078..139653999,6	MCF-7	breast:

No data

Variant related genes	Relation type
CLSTN2	TF binding region
CLSTN2	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs532536014	chr3:139653755-139653756	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs545821028	chr3:139653785-139653786	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs559609442	chr3:139653793-139653794	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs528330062	chr3:139653817-139653818	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs548429967	chr3:139653914-139653915	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
6	rs34435091	chr3:139653928-139653929	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
7	rs146460085	chr3:139653972-139653973	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
8	rs563873565	chr3:139653998-139653999	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs530647525	chr3:139654015-139654016	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs550689526	chr3:139654020-139654021	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs570391029	chr3:139654197-139654198	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs539426386	chr3:139654245-139654246	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs552647225	chr3:139654275-139654276	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs566383695	chr3:139654280-139654281	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs74884664	chr3:139654298-139654299	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:175 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139653200-139654000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:139653200-139654200	Enhancers	Fetal Brain Male	brain
3	chr3:139653200-139654800	Active TSS	Brain Anterior Caudate	brain
4	chr3:139653200-139655000	Active TSS	Brain Cingulate Gyrus	brain
5	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:139653200-139655400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:139653200-139655600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:139653200-139655600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:139653200-139656000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr3:139653400-139653800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:139653400-139653800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
17	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
18	chr3:139653400-139653800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
19	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
20	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
21	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Lung	lung
22	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
23	chr3:139653400-139653800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
24	chr3:139653400-139654000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr3:139653400-139654000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr3:139653400-139654000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
27	chr3:139653400-139654000	Enhancers	Gastric	stomach
28	chr3:139653400-139654000	Bivalent Enhancer	Spleen	Spleen
29	chr3:139653400-139654200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:139653400-139654200	Active TSS	Brain Hippocampus Middle	brain
31	chr3:139653400-139654200	Active TSS	Rectal Smooth Muscle	rectum
32	chr3:139653400-139654200	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr3:139653400-139654400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr3:139653400-139654400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr3:139653400-139654400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:139653400-139654400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:139653400-139654400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:139653400-139654400	Bivalent/Poised TSS	HSMM	muscle
39	chr3:139653400-139654400	Active TSS	NH-A	brain
40	chr3:139653400-139654600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:139653400-139654600	Active TSS	Fetal Brain Female	brain
42	chr3:139653400-139654600	Active TSS	Fetal Kidney	kidney
43	chr3:139653400-139654800	Active TSS	Brain Substantia Nigra	brain
44	chr3:139653400-139655000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
45	chr3:139653400-139655000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:139653400-139655000	Flanking Active TSS	Pancreas	Pancrea
47	chr3:139653400-139655000	Bivalent/Poised TSS	A549	lung
48	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:139653400-139655200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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