Variant report

Variant	nsv348640
Chromosome Location	chr6:46601595-46607072
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	BRCA1	chr6:46606445-46606678	Hela-S3	cervix:	n/a	n/a
2	BRCA1	chr6:46604385-46604409	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr6:46606356-46606757	ECC-1	luminal epithelium:	n/a	n/a
4	CEBPB	chr6:46606358-46606796	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr6:46604891-46605413	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr6:46604954-46605229	MCF-7	breast:	n/a	n/a
7	CEBPB	chr6:46605004-46605259	IMR90	lung:	n/a	n/a
8	CEBPB	chr6:46606427-46606830	ECC-1	luminal epithelium:	n/a	n/a
9	CEBPB	chr6:46606428-46606783	MCF-7	breast:	n/a	n/a
10	CEBPB	chr6:46606330-46606792	HCT-116	colon:	n/a	n/a
11	CEBPB	chr6:46606403-46606767	HCT-116	colon:	n/a	n/a
12	CEBPB	chr6:46603855-46604091	IMR90	lung:	n/a	n/a
13	CEBPB	chr6:46606283-46606766	MCF-7	breast:	n/a	n/a
14	CHD2	chr6:46606375-46606859	Hela-S3	cervix:	n/a	n/a
15	CHD2	chr6:46604822-46605240	Hela-S3	cervix:	n/a	n/a
16	E2F4	chr6:46604925-46605444	MCF10A-Er-Src	breast:	n/a	n/a
17	E2F4	chr6:46606438-46606655	MCF10A-Er-Src	breast:	n/a	n/a
18	EBF1	chr6:46605700-46605928	GM12878	blood:	n/a	chr6:46605833-46605844 chr6:46605832-46605845
19	EP300	chr6:46604925-46605365	Hela-S3	cervix:	n/a	chr6:46605350-46605364
20	EP300	chr6:46606371-46606856	Hela-S3	cervix:	n/a	n/a
21	FOS	chr6:46606370-46606776	MCF10A-Er-Src	breast:	n/a	chr6:46606661-46606671 chr6:46606555-46606565 chr6:46606556-46606564 chr6:46606661-46606671
22	FOS	chr6:46605966-46606154	MCF10A-Er-Src	breast:	n/a	chr6:46606115-46606125
23	FOS	chr6:46604846-46605310	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr6:46604825-46605430	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr6:46604847-46605291	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr6:46606368-46606833	MCF10A-Er-Src	breast:	n/a	chr6:46606661-46606671 chr6:46606555-46606565 chr6:46606556-46606564 chr6:46606661-46606671
27	FOS	chr6:46604797-46605376	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr6:46606016-46606873	MCF10A-Er-Src	breast:	n/a	chr6:46606661-46606671 chr6:46606115-46606125 chr6:46606555-46606565 chr6:46606556-46606564 chr6:46606661-46606671
29	FOS	chr6:46606388-46606770	MCF10A-Er-Src	breast:	n/a	chr6:46606661-46606671 chr6:46606555-46606565 chr6:46606556-46606564 chr6:46606661-46606671
30	FOXA1	chr6:46602572-46602808	T-47D	breast:	n/a	n/a
31	JUN	chr6:46606687-46606850	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAFK	chr6:46606362-46606730	Hela-S3	cervix:	n/a	n/a
33	MAFK	chr6:46606508-46606562	HepG2	liver:	n/a	n/a
34	MAFK	chr6:46606495-46606563	HepG2	liver:	n/a	n/a
35	MAX	chr6:46604901-46605293	Hela-S3	cervix:	n/a	n/a
36	MAX	chr6:46606310-46606752	ECC-1	luminal epithelium:	n/a	chr6:46606445-46606455
37	MAX	chr6:46606427-46606774	Hela-S3	cervix:	n/a	chr6:46606445-46606455
38	MXI1	chr6:46604945-46605168	Hela-S3	cervix:	n/a	n/a
39	MYC	chr6:46606402-46606741	MCF10A-Er-Src	breast:	n/a	chr6:46606445-46606455
40	MYC	chr6:46604616-46605378	MCF10A-Er-Src	breast:	n/a	n/a
41	MYC	chr6:46606388-46606842	MCF10A-Er-Src	breast:	n/a	chr6:46606445-46606455
42	MYC	chr6:46604811-46605374	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr6:46601948-46602009	Gliobla	brain:	n/a	n/a
44	POLR2A	chr6:46604858-46605786	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr6:46604385-46605822	Raji	blood:	n/a	n/a
46	POLR2A	chr6:46604748-46606911	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr6:46606107-46606855	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr6:46603884-46603912	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:46603960-46604031	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:46603991-46604106	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:46606337..46609019-chr6:46614222..46616083,2	MCF-7	breast:

Variant related genes	Relation type
CYP39A1	TF binding region

Extended variants
information (count: 211 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:211 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11442056	chr6:46601600-46601601	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs565867814	chr6:46601611-46601612	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs1234166	chr6:46601651-46601652	Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs186459879	chr6:46601671-46601672	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs548591785	chr6:46601677-46601678	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs576187170	chr6:46601698-46601699	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs537092299	chr6:46601702-46601703	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs141907000	chr6:46601803-46601804	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs146032242	chr6:46601812-46601813	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs561016816	chr6:46601823-46601824	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs541714822	chr6:46601853-46601854	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs191765715	chr6:46601885-46601886	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs545181357	chr6:46601886-46601887	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs563469510	chr6:46601901-46601902	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs13216565	chr6:46601912-46601913	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs372101253	chr6:46601959-46601960	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs148263342	chr6:46602004-46602005	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs561342622	chr6:46602060-46602061	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs528427105	chr6:46602106-46602107	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs181440981	chr6:46602148-46602149	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs377406962	chr6:46602154-46602155	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs186456907	chr6:46602243-46602244	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs147533342	chr6:46602244-46602245	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs202066009	chr6:46602254-46602255	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs530045412	chr6:46602260-46602261	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs9472811	chr6:46602261-46602262	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs55887439	chr6:46602262-46602263	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs70996382	chr6:46602277-46602278	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs551601437	chr6:46602319-46602320	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs190887545	chr6:46602320-46602321	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs182370389	chr6:46602330-46602331	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs367619412	chr6:46602340-46602341	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs187688065	chr6:46602344-46602345	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs534288833	chr6:46602345-46602346	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs553663750	chr6:46602396-46602397	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs577894191	chr6:46602403-46602404	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs190964583	chr6:46602405-46602406	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs557121919	chr6:46602478-46602479	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs575390784	chr6:46602536-46602537	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs371675834	chr6:46602539-46602540	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs16874904	chr6:46602563-46602564	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs528499179	chr6:46602634-46602635	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs540245566	chr6:46602684-46602685	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs528542627	chr6:46602698-46602699	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs114242378	chr6:46602882-46602883	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs551662927	chr6:46602942-46602943	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs139110668	chr6:46602967-46602968	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs530698769	chr6:46603003-46603004	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs549078291	chr6:46603041-46603042	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs567234189	chr6:46603059-46603060	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Melanoma	18172304	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	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
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
Osteosarcoma	21197465	CNVD
Gastric cancer	24379144	CNVD
Neuroblastoma	18923191	CNVD
abnormal development	18461090	CNVD
Breast cancer	17603634	CNVD
Breast cancer	21364760	CNVD
Follicular lymphoma	16790693	CNVD
Osteosarcoma	19286668	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Myelofibrosis	22110671	CNVD
Heart disease	21282601	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	16608533	CNVD
Olfactory neuroblastoma	18408657	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46580800-46619600	Weak transcription	Psoas Muscle	Psoas
2	chr6:46590400-46603000	Weak transcription	Fetal Stomach	stomach
3	chr6:46591200-46604400	Weak transcription	Fetal Lung	lung
4	chr6:46592200-46609200	Weak transcription	Ovary	ovary
5	chr6:46599800-46603400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:46600600-46610600	Weak transcription	Liver	Liver
7	chr6:46601400-46608000	Weak transcription	Aorta	Aorta
8	chr6:46602000-46602200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:46602400-46605000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:46603000-46603600	Strong transcription	Fetal Stomach	stomach
11	chr6:46603400-46605200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:46603600-46604800	Weak transcription	Fetal Stomach	stomach
13	chr6:46604400-46605000	Enhancers	Placenta	Placenta
14	chr6:46604400-46605400	Enhancers	Fetal Lung	lung
15	chr6:46604400-46605600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:46604400-46605800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:46604400-46605800	Enhancers	NHDF-Ad	bronchial
18	chr6:46604400-46606200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:46604400-46607000	Enhancers	HMEC	breast
20	chr6:46604600-46604800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:46604600-46605000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:46604600-46605000	Enhancers	Adipose Nuclei	Adipose
23	chr6:46604600-46605400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:46604600-46605400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:46604600-46605400	Enhancers	HSMMtube	muscle
26	chr6:46604600-46605600	Enhancers	Fetal Brain Male	brain
27	chr6:46604600-46606600	Enhancers	NHEK	skin
28	chr6:46604600-46606800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:46604600-46607200	Enhancers	Hela-S3	cervix
30	chr6:46604800-46605000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:46604800-46605200	Enhancers	Fetal Stomach	stomach
32	chr6:46604800-46605400	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:46604800-46605600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:46605000-46605200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:46605000-46606600	Weak transcription	Placenta	Placenta
36	chr6:46605000-46611200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:46605200-46605400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:46605200-46605600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr6:46605400-46605600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:46605600-46606600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:46605600-46610600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:46605600-46611000	Weak transcription	Fetal Brain Male	brain
43	chr6:46606200-46606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:46606400-46606800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr6:46606400-46606800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr6:46606400-46606800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr6:46606600-46606800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:46606600-46606800	Enhancers	Placenta	Placenta
49	chr6:46606600-46607000	Flanking Active TSS	NHEK	skin
50	chr6:46606600-46607600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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