Variant report

Variant	esv3356917
Chromosome Location	chr6:72090881-72093079
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	CTCF	chr6:72092980-72093130	GM06990	blood:	n/a	n/a
2	CTCF	chr6:72092973-72094229	SK-N-SH	brain:	n/a	chr6:72093774-72093792 chr6:72093776-72093797 chr6:72093777-72093786 chr6:72093775-72093791
3	EBF1	chr6:72090819-72091023	GM12878	blood:	n/a	chr6:72090912-72090922 chr6:72090912-72090921 chr6:72090910-72090921 chr6:72090912-72090921 chr6:72090910-72090923
4	EGR1	chr6:72093055-72093267	K562	blood:	n/a	n/a
5	IRF1	chr6:72092179-72092206	K562	blood:	n/a	n/a
6	POLR2A	chr6:72092505-72096424	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:72090217-72091083	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr6:72092930-72093576	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:72090840-72090888	Hela-S3	cervix:	n/a	n/a
10	RAD21	chr6:72092831-72094275	SK-N-SH	brain:	n/a	chr6:72093775-72093794 chr6:72093776-72093785
11	SPI1	chr6:72090782-72091000	HL-60	blood:	n/a	chr6:72090881-72090890 chr6:72090879-72090892 chr6:72090880-72090893 chr6:72090882-72090889
12	SPI1	chr6:72090811-72090989	K562	blood:	n/a	chr6:72090881-72090890 chr6:72090879-72090892 chr6:72090880-72090893 chr6:72090882-72090889

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GAT2-3	chr6:72090722-72091307	NONHSAT113497

Variant related genes	Relation type
MIR30C2	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:102 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs192185442	chr6:72090905-72090906	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs9446385	chr6:72090908-72090909	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs544371806	chr6:72090919-72090920	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs565791636	chr6:72090936-72090937	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs556842944	chr6:72090938-72090939	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs575040396	chr6:72090939-72090940	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs1192041	chr6:72090956-72090957	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs12174570	chr6:72090988-72090989	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs557757739	chr6:72090994-72090995	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs528098903	chr6:72090998-72090999	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs540252194	chr6:72091029-72091030	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs564716087	chr6:72091077-72091078	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs575981844	chr6:72091092-72091093	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs532279017	chr6:72091134-72091135	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs200993326	chr6:72091183-72091184	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs183436802	chr6:72091236-72091237	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs537035480	chr6:72091257-72091258	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs5877279	chr6:72091267-72091268	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs3071015	chr6:72091268-72091269	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs397716752	chr6:72091282-72091283	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs70990369	chr6:72091308-72091309	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs144831611	chr6:72091314-72091315	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs555829240	chr6:72091346-72091347	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs185826991	chr6:72091360-72091361	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs9446386	chr6:72091416-72091417	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs12174599	chr6:72091444-72091445	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs548099758	chr6:72091450-72091451	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs12174600	chr6:72091472-72091473	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs9717724	chr6:72091500-72091501	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs577727609	chr6:72091514-72091515	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs9717684	chr6:72091528-72091529	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs145625139	chr6:72091556-72091557	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs566785796	chr6:72091562-72091563	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs186898389	chr6:72091567-72091568	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs557716001	chr6:72091575-72091576	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs371672647	chr6:72091582-72091583	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs192774945	chr6:72091593-72091594	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs368504337	chr6:72091602-72091603	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs375070175	chr6:72091609-72091610	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs182751362	chr6:72091620-72091621	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs370674038	chr6:72091647-72091648	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs538340133	chr6:72091871-72091872	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs70990370	chr6:72091872-72091873	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs563779857	chr6:72091893-72091894	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs575104311	chr6:72091894-72091895	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs542415835	chr6:72091898-72091899	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs70990371	chr6:72091899-72091900	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs372870159	chr6:72091926-72091927	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs554387346	chr6:72091947-72091948	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs376477186	chr6:72091953-72091954	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Systemic lupus erythematosus	17503323	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Melanoma	18172304	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Cancer	21637783	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
T-cell lymphomas	19863542	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	19010834	CNVD
Non-small cell lung cancer	21044232	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21385341	CNVD
Prostate cancer	16705090	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Ependymoma	16718352	CNVD
High-proliferative meningiomas	17937814	CNVD
Intracranial tumor	16823260	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Prostate cancer	16573809	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	16272173	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Urothelial carcinoma	18382360	CNVD
Ovarian neoplasms	16753589	CNVD
Hepatocellular carcinoma	16750200	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	17437010	CNVD
Myelofibrosis	22110671	CNVD
Glioma	17123091	CNVD
Mental retardation	17124404	CNVD
Chondromyxoid Fibroma	20696777	CNVD
Multiple myeloma	16616336	CNVD
Acute myeloid leukemia	16864856	CNVD
Follicular lymphoma	17699855	CNVD
Breast cancer	17133270	CNVD
Leukemia	18688285	CNVD
Prostate cancer	19242612	CNVD
Breast cancer	20409316	CNVD

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:72061600-72097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:72076000-72093400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:72076200-72103200	Weak transcription	Aorta	Aorta
4	chr6:72077600-72093400	Weak transcription	Brain Anterior Caudate	brain
5	chr6:72077600-72094800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:72077800-72093000	Weak transcription	Lung	lung
7	chr6:72077800-72093200	Weak transcription	Pancreas	Pancrea
8	chr6:72077800-72097000	Weak transcription	Psoas Muscle	Psoas
9	chr6:72077800-72097200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:72078200-72095400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:72079800-72098800	Weak transcription	Brain Substantia Nigra	brain
12	chr6:72081400-72091400	Strong transcription	Hela-S3	cervix
13	chr6:72082600-72093200	Weak transcription	Osteobl	bone
14	chr6:72083400-72094600	Weak transcription	Fetal Intestine Large	intestine
15	chr6:72083800-72097800	Weak transcription	Placenta	Placenta
16	chr6:72084200-72097000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:72084200-72106600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:72084400-72092600	Weak transcription	Fetal Lung	lung
19	chr6:72084400-72093400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:72084400-72094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:72084400-72094800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:72084400-72099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:72085400-72091000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:72085600-72096800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:72085800-72105400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:72086200-72091000	Strong transcription	HSMM	muscle
27	chr6:72086200-72093000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:72087000-72093200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:72087400-72091000	Strong transcription	HMEC	breast
30	chr6:72087400-72098200	Weak transcription	Colonic Mucosa	Colon
31	chr6:72087600-72091000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:72088000-72092400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:72088000-72093400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:72088400-72097800	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:72088600-72093000	Weak transcription	Left Ventricle	heart
36	chr6:72088600-72093600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:72088600-72097000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:72088800-72091200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:72088800-72092200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:72088800-72093200	Weak transcription	Right Ventricle	heart
41	chr6:72088800-72095000	Weak transcription	HSMMtube	muscle
42	chr6:72088800-72101000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:72089000-72092600	Weak transcription	HUVEC	blood vessel
44	chr6:72089000-72093800	Weak transcription	Liver	Liver
45	chr6:72090400-72091200	Enhancers	Adipose Nuclei	Adipose
46	chr6:72090400-72091200	Genic enhancers	Fetal Kidney	kidney
47	chr6:72090400-72091200	Strong transcription	NHEK	skin
48	chr6:72090400-72091400	Strong transcription	NH-A	brain
49	chr6:72090400-72101000	Weak transcription	Gastric	stomach
50	chr6:72090600-72091000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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