Variant report

Variant	esv3368559
Chromosome Location	chr3:98516554-98517123
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr3:98516705-98517120	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
3	POLR2A	chr3:98516882-98516891	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:98516282-98517180	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:98516760-98516814	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
7	POLR2A	chr3:98517007-98517156	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:98516148-98517038	A549	lung:	n/a	n/a
9	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a
10	POLR2A	chr3:98516817-98516828	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:98516179-98518840	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:98516641-98516893	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:98517048-98517098	AG04449	skin:	fetal
2	chr3:98517048-98517098	SK-N-MC	brain:	n/a
3	chr3:98517048-98517098	NHDF-neo	bronchial:	n/a
4	chr3:98517048-98517098	GM12892	blood:	n/a
5	chr3:98517048-98517098	RPTEC	kidney:	n/a
6	chr3:98517048-98517098	HAEpiC	amniotic membrane:	n/a
7	chr3:98517048-98517098	ProgFib	skin:	n/a
8	chr3:98517048-98517098	MCF10A-Er-Src	breast:	n/a
9	chr3:98517048-98517098	NB4	blood:	n/a
10	chr3:98517048-98517098	AG09319	gingival:	n/a
11	chr3:98517048-98517098	HPAEpiC	pulmonary alveolar:	n/a
12	chr3:98517048-98517098	K562	blood:	n/a
13	chr3:98517048-98517098	Hepatocyte	liver:	n/a
14	chr3:98517048-98517098	PANC-1	pancreas:	n/a
15	chr3:98517048-98517098	AG09309	skin:	n/a
16	chr3:98517048-98517098	Hela-S3	cervix:	n/a
17	chr3:98517048-98517098	HUVEC	blood vessel:	n/a
18	chr3:98517048-98517098	AG10803	skin:	n/a
19	chr3:98517048-98517098	HCPEpiC	choroid plexus:	n/a
20	chr3:98517048-98517098	ovcar-3	ovarian:	n/a
21	chr3:98517048-98517098	HRPEpiC	eye:	n/a
22	chr3:98517048-98517098	T-47D	breast:	n/a
23	chr3:98517048-98517098	U87	brain:	n/a
24	chr3:98517048-98517098	HL-60	blood:	n/a
25	chr3:98517048-98517098	GM12891	blood:	n/a
26	chr3:98517048-98517098	PrEC	prostate:	n/a
27	chr3:98517048-98517098	HepG2	liver:	n/a
28	chr3:98517048-98517098	HMEC	breast:	n/a
29	chr3:98517048-98517098	HNPCEpiC	eye:	n/a
30	chr3:98517048-98517098	HEEpiC	esophagus:	n/a
31	chr3:98517048-98517098	H1-hESC	embryonic stem cell:	embryo
32	chr3:98517048-98517098	HRE	kidney:	n/a
33	chr3:98517048-98517098	GM19239	blood:	n/a
34	chr3:98517048-98517098	GM12878	blood:	n/a
35	chr3:98517048-98517098	LNCaP	prostate:	n/a
36	chr3:98517048-98517098	AG04450	lung:	fetal
37	chr3:98517048-98517098	SK-N-SH_RA	brain:	n/a
38	chr3:98517048-98517098	SK-N-SH	brain:	n/a
39	chr3:98517048-98517098	AoSMC	blood vessel:	n/a
40	chr3:98517048-98517098	NH-A	brain:	n/a
41	chr3:98517048-98517098	HRCEpiC	kidney:	n/a
42	chr3:98517048-98517098	A549	lung:	n/a
43	chr3:98517048-98517098	MCF-7	breast:	n/a
44	chr3:98517048-98517098	HCF	heart:	n/a
45	chr3:98517048-98517098	HCM	heart:	n/a
46	chr3:98517048-98517098	IMR90	lung:	fetal
47	chr3:98517048-98517098	HIPEpiC	eye:	n/a
48	chr3:98517048-98517098	ECC-1	luminal epithelium:	n/a
49	chr3:98517048-98517098	BJ	skin:	n/a
50	chr3:98517048-98517098	NHBE	bronchial:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98505121..98508904-chr3:98514678..98518486,3	MCF-7	breast:

No data

Variant related genes	Relation type
ST3GAL6	TF binding region
ST3GAL6	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs141830183	chr3:98516555-98516556	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs577117348	chr3:98516582-98516583	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs538425755	chr3:98516596-98516597	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs147088567	chr3:98516605-98516606	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs562459402	chr3:98516606-98516607	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs531469637	chr3:98516652-98516653	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs1062197	chr3:98516760-98516761	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs189199051	chr3:98516762-98516763	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs138443323	chr3:98516821-98516822	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs542907641	chr3:98516845-98516846	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs111421350	chr3:98516860-98516861	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs566697199	chr3:98516956-98516957	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs368943056	chr3:98516960-98516961	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs828607	chr3:98516981-98516982	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs569228692	chr3:98516986-98516987	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs1062196	chr3:98517013-98517014	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs562238289	chr3:98517032-98517033	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs554655165	chr3:98517048-98517049	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
19	rs192015188	chr3:98517067-98517068	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	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
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
4	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
7	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
8	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
9	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
11	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
12	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:98503400-98518200	Weak transcription	Ovary	ovary
15	chr3:98503400-98576400	Weak transcription	Gastric	stomach
16	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:98504600-98517000	Weak transcription	HSMMtube	muscle
18	chr3:98504600-98519400	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
20	chr3:98504800-98517400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:98505400-98518400	Weak transcription	Fetal Thymus	thymus
23	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
24	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
25	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
26	chr3:98506200-98518000	Weak transcription	Fetal Intestine Large	intestine
27	chr3:98506400-98519400	Weak transcription	Brain Anterior Caudate	brain
28	chr3:98506400-98524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:98506800-98523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:98507800-98517400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:98507800-98517400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:98507800-98518200	Weak transcription	Right Ventricle	heart
33	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
34	chr3:98508000-98516600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:98508000-98519600	Weak transcription	Fetal Lung	lung
36	chr3:98508000-98524600	Weak transcription	GM12878-XiMat	blood
37	chr3:98508200-98524600	Weak transcription	Fetal Heart	heart
38	chr3:98511400-98518400	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:98512200-98521000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:98512400-98520800	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr3:98512800-98520400	Strong transcription	HSMM	muscle
42	chr3:98513000-98520800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:98513000-98524400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:98513400-98520600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:98513400-98520800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:98513400-98520800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:98513400-98523800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:98513600-98516800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:98513600-98520800	Strong transcription	NH-A	brain
50	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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