Variant report

Variant	nsv1026300
Chromosome Location	chr6:66394090-66423054
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	CEBPB	chr6:66404594-66404863	HepG2	liver:	n/a	chr6:66404777-66404786 chr6:66404777-66404786 chr6:66404777-66404786
2	CEBPB	chr6:66404687-66404887	H1-hESC	embryonic stem cell:	n/a	chr6:66404777-66404786 chr6:66404777-66404786 chr6:66404777-66404786
3	CEBPB	chr6:66404649-66404900	K562	blood:	n/a	chr6:66404777-66404786 chr6:66404777-66404786 chr6:66404777-66404786
4	CEBPB	chr6:66404609-66404903	IMR90	lung:	n/a	chr6:66404777-66404786 chr6:66404777-66404786 chr6:66404777-66404786
5	CTCF	chr6:66410644-66410670	Lung_OC	lung:	n/a	n/a
6	CTCF	chr6:66413711-66413749	Spleen_OC	spleen:	n/a	n/a
7	E2F4	chr6:66408749-66408935	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr6:66416771-66417877	SK-N-SH	brain:	n/a	n/a
9	EP300	chr6:66416982-66417333	SK-N-SH_RA	brain:	n/a	n/a
10	FOS	chr6:66395537-66395830	MCF10A-Er-Src	breast:	n/a	chr6:66395682-66395689 chr6:66395679-66395691 chr6:66395680-66395690 chr6:66395681-66395690 chr6:66395681-66395689
11	FOS	chr6:66395517-66395831	MCF10A-Er-Src	breast:	n/a	chr6:66395682-66395689 chr6:66395679-66395691 chr6:66395680-66395690 chr6:66395681-66395690 chr6:66395681-66395689
12	FOXA1	chr6:66416372-66416623	HepG2	liver:	n/a	chr6:66416405-66416417
13	FOXA1	chr6:66421704-66421924	T-47D	breast:	n/a	n/a
14	FOXA2	chr6:66416409-66416701	A549	lung:	n/a	n/a
15	GATA3	chr6:66417270-66417611	SH-SY5Y	brain:	n/a	n/a
16	GATA3	chr6:66399966-66400276	T-47D	breast:	n/a	n/a
17	GATA3	chr6:66400055-66400362	T-47D	breast:	n/a	n/a
18	IRF1	chr6:66410728-66410812	K562	blood:	n/a	n/a
19	JUND	chr6:66395561-66395796	HepG2	liver:	n/a	chr6:66395682-66395689 chr6:66395679-66395691 chr6:66395680-66395690 chr6:66395681-66395690 chr6:66395681-66395689 chr6:66395679-66395690
20	MAFF	chr6:66421445-66421784	K562	blood:	n/a	chr6:66421607-66421625
21	MAFF	chr6:66421433-66421809	HepG2	liver:	n/a	chr6:66421607-66421625
22	MAFF	chr6:66412135-66412204	HepG2	liver:	n/a	n/a
23	MAFK	chr6:66421437-66421802	IMR90	lung:	n/a	chr6:66421609-66421624
24	MAFK	chr6:66421427-66421794	HepG2	liver:	n/a	chr6:66421609-66421624
25	MAFK	chr6:66421428-66421817	HepG2	liver:	n/a	chr6:66421609-66421624
26	MAFK	chr6:66421446-66421780	K562	blood:	n/a	chr6:66421609-66421624
27	MAFK	chr6:66421438-66421764	Hela-S3	cervix:	n/a	chr6:66421609-66421624
28	MAFK	chr6:66421487-66421762	H1-hESC	embryonic stem cell:	n/a	chr6:66421609-66421624
29	MXI1	chr6:66416797-66417835	SK-N-SH	brain:	n/a	chr6:66417489-66417504 chr6:66417491-66417506
30	MYC	chr6:66398465-66398522	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:66417339-66417707	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr6:66416908-66417326	H1-neurons	neurons:	n/a	n/a
33	POLR2A	chr6:66416896-66417807	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr6:66411108-66411293	MCF10A-Er-Src	breast:	n/a	n/a
35	REST	chr6:66416834-66418001	H1-neurons	neurons:	n/a	n/a
36	SPI1	chr6:66397389-66397529	K562	blood:	n/a	n/a
37	SPI1	chr6:66397432-66397586	K562	blood:	n/a	n/a
38	STAT3	chr6:66410550-66410750	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr6:66401979-66402200	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr6:66421416-66421448	MCF10A-Er-Src	breast:	n/a	n/a
41	STAT3	chr6:66415402-66415503	MCF10A-Er-Src	breast:	n/a	n/a
42	TCF12	chr6:66416241-66416820	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:189034137..189034728-chr6:66401890..66402666,2	MCF-7	breast:
2	chr6:66389053..66391661-chr6:66392622..66394298,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LGSN-7	chr6:66417028-66417107	NONHSAT113373

Variant related genes	Relation type
EYS	TF binding region

Extended variants
information (count: 618 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:618 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9294645	chr6:66394090-66394091	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs79527468	chr6:66394110-66394111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs143465982	chr6:66394127-66394128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs534096371	chr6:66394135-66394136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs539048438	chr6:66394150-66394151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs10944833	chr6:66394158-66394159	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs572842603	chr6:66394173-66394174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs541644910	chr6:66394176-66394177	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs16897048	chr6:66394196-66394197	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs114902360	chr6:66394209-66394210	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs180826594	chr6:66394212-66394213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs564582591	chr6:66394215-66394216	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs185962409	chr6:66394244-66394245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs61422784	chr6:66394252-66394253	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs560749662	chr6:66394256-66394257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs75287117	chr6:66394259-66394260	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs549431333	chr6:66394273-66394274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs191259367	chr6:66394280-66394281	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs146734395	chr6:66394281-66394282	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs550213210	chr6:66394302-66394303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs139132330	chr6:66394312-66394313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs539037873	chr6:66394330-66394331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs552584960	chr6:66394339-66394340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs149908773	chr6:66394361-66394362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs535713592	chr6:66394366-66394367	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs555392357	chr6:66394386-66394387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs116306439	chr6:66394392-66394393	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs533610936	chr6:66394393-66394394	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs558282833	chr6:66394440-66394441	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs144923381	chr6:66394464-66394465	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs200427782	chr6:66394490-66394491	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs540606965	chr6:66394535-66394536	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs560482841	chr6:66394544-66394545	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs529284591	chr6:66394551-66394552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs543264301	chr6:66394583-66394584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs76818562	chr6:66394587-66394588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs1490123	chr6:66394589-66394590	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs1490124	chr6:66394598-66394599	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs372883972	chr6:66394648-66394649	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs576112936	chr6:66394726-66394727	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs181326305	chr6:66394727-66394728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs2130492	chr6:66394762-66394763	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs186852175	chr6:66394797-66394798	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs532897719	chr6:66394809-66394810	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs1490125	chr6:66394859-66394860	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs566434567	chr6:66394885-66394886	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs75987232	chr6:66394890-66394891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs555593495	chr6:66394924-66394925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs569095443	chr6:66394925-66394926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs538032854	chr6:66394976-66394977	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

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
Malignant peripheral nerve sheath tumor	18522746	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
T-cell lymphomas	19863542	CNVD
Oral squamous cell carcinoma	17134496	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
Breast cancer	21364760	CNVD
Prostate cancer	16573809	CNVD
Ovarian cancer	19835627	CNVD
Myelofibrosis	22110671	CNVD
Cancer	21183584	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	16272173	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	20016488	CNVD
Multiple myeloma	17550852	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
Cancer	20164919	CNVD
Retinitis pigmentosa	21519034	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:66393800-66396000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:66396000-66396200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:66396200-66396600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:66399600-66400400	Enhancers	Placenta	Placenta
5	chr6:66401800-66402200	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr6:66402200-66403400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:66403600-66403800	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr6:66408400-66408800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:66408800-66409200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:66409200-66412000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:66410000-66411000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:66410000-66411200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr6:66410400-66411000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr6:66410600-66411000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr6:66411000-66411400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:66411400-66412800	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr6:66412800-66413600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:66413600-66413800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr6:66413800-66414000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:66413800-66414800	Enhancers	A549	lung
21	chr6:66414000-66414400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr6:66414400-66414800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:66414800-66415200	Weak transcription	A549	lung
24	chr6:66414800-66415400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr6:66415000-66415200	Enhancers	Fetal Intestine Small	intestine
26	chr6:66415000-66415600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:66415200-66415400	Enhancers	A549	lung
28	chr6:66415400-66416400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:66415400-66416400	Weak transcription	A549	lung
30	chr6:66415600-66416400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:66415600-66416600	Weak transcription	Fetal Intestine Small	intestine
32	chr6:66416200-66416400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:66416400-66416600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr6:66416400-66416800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:66416400-66416800	Enhancers	A549	lung
36	chr6:66416400-66417400	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr6:66416400-66418400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:66416600-66417000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr6:66416600-66417200	Enhancers	Fetal Intestine Small	intestine
40	chr6:66416800-66418400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:66417000-66417200	Enhancers	Fetal Brain Male	brain
42	chr6:66417000-66417400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr6:66417000-66417400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr6:66417000-66417400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr6:66417000-66417400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:66417000-66417600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:66417000-66417800	Enhancers	Fetal Brain Female	brain
48	chr6:66417200-66418200	Weak transcription	Fetal Brain Male	brain
49	chr6:66417600-66418200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:66418200-66418600	Enhancers	Fetal Brain Male	brain

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