Variant report

Variant	nsv970988
Chromosome Location	chr7:39804754-39819869
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	BATF	chr7:39813857-39814230	GM12878	blood:	n/a	n/a
2	BATF	chr7:39813917-39814187	GM12878	blood:	n/a	n/a
3	CEBPB	chr7:39810290-39810355	IMR90	lung:	n/a	n/a
4	CEBPB	chr7:39816708-39817080	HepG2	liver:	n/a	chr7:39816882-39816893
5	CEBPB	chr7:39816765-39817021	IMR90	lung:	n/a	chr7:39816882-39816893
6	CEBPB	chr7:39816783-39817025	A549	lung:	n/a	chr7:39816882-39816893
7	CEBPB	chr7:39816708-39817032	K562	blood:	n/a	chr7:39816882-39816893
8	CTCF	chr7:39815110-39815169	GM13976	blood:	n/a	n/a
9	EP300	chr7:39805669-39806112	SK-N-SH_RA	brain:	n/a	chr7:39805935-39805949 chr7:39805702-39805710
10	EP300	chr7:39805614-39806111	SK-N-SH_RA	brain:	n/a	chr7:39805935-39805949 chr7:39805702-39805710
11	FOSL2	chr7:39818910-39819228	HepG2	liver:	n/a	chr7:39819125-39819136
12	FOSL2	chr7:39818913-39819339	HepG2	liver:	n/a	chr7:39819125-39819136
13	IRF4	chr7:39813933-39814199	GM12878	blood:	n/a	n/a
14	PAX5	chr7:39813834-39814221	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:39813314-39813461	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:39812328-39812560	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:39812816-39812832	Hela-S3	cervix:	n/a	n/a
18	REST	chr7:39813916-39814304	U87	brain:	n/a	n/a
19	REST	chr7:39814037-39814315	PANC-1	pancreas:	n/a	n/a
20	REST	chr7:39813921-39814499	GM12878	blood:	n/a	n/a
21	REST	chr7:39813987-39814402	HepG2	liver:	n/a	n/a
22	REST	chr7:39814049-39814237	HepG2	liver:	n/a	n/a
23	REST	chr7:39813976-39814378	U87	brain:	n/a	n/a
24	REST	chr7:39813934-39814372	H1-hESC	embryonic stem cell:	n/a	n/a
25	REST	chr7:39813927-39814353	H1-hESC	embryonic stem cell:	n/a	n/a
26	REST	chr7:39814037-39814351	GM12878	blood:	n/a	n/a
27	REST	chr7:39814058-39814297	U87	brain:	n/a	n/a
28	REST	chr7:39814086-39814286	GM12878	blood:	n/a	n/a
29	REST	chr7:39814195-39814333	ECC-1	luminal epithelium:	n/a	n/a
30	REST	chr7:39814170-39814372	ECC-1	luminal epithelium:	n/a	n/a
31	REST	chr7:39814038-39814335	SK-N-SH	brain:	n/a	n/a
32	REST	chr7:39813996-39814377	SK-N-SH	brain:	n/a	n/a
33	REST	chr7:39813965-39814436	PFSK-1	brain:	n/a	n/a
34	REST	chr7:39813944-39814557	PFSK-1	brain:	n/a	n/a
35	REST	chr7:39814087-39814253	K562	blood:	n/a	n/a
36	REST	chr7:39813992-39814295	HepG2	liver:	n/a	n/a
37	REST	chr7:39814039-39814336	PFSK-1	brain:	n/a	n/a
38	REST	chr7:39814101-39814163	K562	blood:	n/a	n/a
39	REST	chr7:39813951-39814439	PFSK-1	brain:	n/a	n/a
40	REST	chr7:39814078-39814276	PANC-1	pancreas:	n/a	n/a
41	SP1	chr7:39818884-39819246	HepG2	liver:	n/a	n/a
42	SPI1	chr7:39819719-39819896	K562	blood:	n/a	chr7:39819793-39819806 chr7:39819794-39819807 chr7:39819796-39819805
43	TCF12	chr7:39813774-39814090	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf11-2	chr7:39807001-39807261	XLOC_006416
2	lnc-RALA-1	chr7:39818870-39819091	XLOC_006057
3	lnc-RALA-1	chr7:39811849-39812029	XLOC_006057

Variant related genes	Relation type
LINC00265	TF binding region
RNU6-719P	TF binding region
SMARCD1	miRNA target sites

Extended variants
information (count: 608 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:608 , 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	rs558152824	chr7:39804834-39804835	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs542903423	chr7:39804837-39804838	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs543624466	chr7:39804847-39804848	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs563554502	chr7:39804860-39804861	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs193011696	chr7:39804923-39804924	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs185736064	chr7:39804964-39804965	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs149955800	chr7:39804993-39804994	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs528465192	chr7:39804995-39804996	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs560993171	chr7:39805016-39805017	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs189959385	chr7:39805040-39805041	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs147654112	chr7:39805049-39805050	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs578181635	chr7:39805194-39805195	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs70996839	chr7:39805195-39805196	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs398004486	chr7:39805205-39805206	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs142279136	chr7:39805222-39805223	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs377033568	chr7:39805226-39805227	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs550756502	chr7:39805241-39805242	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs567474248	chr7:39805257-39805258	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs536499072	chr7:39805262-39805263	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs73377491	chr7:39805275-39805276	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs145911965	chr7:39805284-39805285	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs558545180	chr7:39805297-39805298	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs578161962	chr7:39805340-39805341	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs537758049	chr7:39805414-39805415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs575980010	chr7:39805453-39805454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs113413441	chr7:39805559-39805560	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs111614163	chr7:39805564-39805565	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs4052223	chr7:39805616-39805617	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs181711295	chr7:39805621-39805622	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs573891788	chr7:39805625-39805626	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs542852006	chr7:39805655-39805656	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs2876870	chr7:39805698-39805699	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs183901442	chr7:39805721-39805722	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs188686020	chr7:39805763-39805764	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs545043301	chr7:39805784-39805785	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs545705167	chr7:39805793-39805794	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs375554901	chr7:39805818-39805819	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs551316836	chr7:39805822-39805823	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs181252757	chr7:39805869-39805870	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs530671611	chr7:39805909-39805910	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs149156670	chr7:39806012-39806013	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs527628066	chr7:39806092-39806093	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs530776603	chr7:39806105-39806106	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs185762704	chr7:39806169-39806170	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs546845861	chr7:39806181-39806182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs566417472	chr7:39806212-39806213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs189489237	chr7:39806233-39806234	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs551846825	chr7:39806234-39806235	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs182066173	chr7:39806246-39806247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs141437046	chr7:39806254-39806255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Biliary cancer	19435499	CNVD
Cancer	16751803	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	17387387	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	18923191	CNVD
Glioma	21971842	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
colon cancer	17210682	CNVD
Lung adenocarcinoma	21810691	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Colorectal cancer	19359472	CNVD
Hypothalamic hamartomas	18252217	CNVD
Human rectal carcinomas	16397240	CNVD
Peripheral t-cell lymphoma	19118030	CNVD
Medulloblastoma	18056178	CNVD
Basal cell lymphoma	17170743	CNVD
Ewing''s sarcoma	21437220	CNVD
Thyroid cancer	19087340	CNVD
Seminomas	18059402	CNVD
Testicular cancer	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	19415332	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
T-cell lymphomas	19863542	CNVD
Malaria	21533027	CNVD
Melanoma	18172304	CNVD
Renal cell carcinoma	19461508	CNVD
head and neck squamous cell carcinoma	19289630	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Cancer	21637783	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16397240	CNVD
Non-small cell lung cancer	21829676	CNVD
Glioblastoma multiforme	17002787	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Glioblastoma multiforme	18628472	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Follicular lymphoma	20505157	CNVD
Williams-beuren syndrome	22470819	CNVD
Renal cell carcinoma	18765545	CNVD
Breast cancer	21364760	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Multiple myeloma	16461302	CNVD
Glioblastoma multiforme	21750150	CNVD
Hepatocellular carcinoma	16750200	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	17237825	CNVD
Breast cancer	17899364	CNVD
Breast cancer	20409316	CNVD
Acute monocytic leukemia	16498392	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	21645411	CNVD
Colorectal cancer	19455253	CNVD
Glioblastoma multiforme	22286061	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Gastric cancer	24379144	CNVD
small cell lung cancer	20016488	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Pancreatic cancer	17952125	CNVD
Bladder cancer	21909424	CNVD

Chromatin state (count:171 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39774200-39807400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:39775800-39807000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr7:39775800-39811200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:39776600-39820400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:39782400-39809000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:39785000-39831800	Weak transcription	Primary B cells from cord blood	blood
7	chr7:39789600-39807200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:39794000-39830800	Weak transcription	Pancreas	Pancrea
9	chr7:39794200-39820800	Weak transcription	Ovary	ovary
10	chr7:39794200-39837400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:39794600-39808800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:39794600-39810200	Weak transcription	Fetal Stomach	stomach
13	chr7:39794600-39830800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:39795200-39807400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:39795400-39813000	Weak transcription	GM12878-XiMat	blood
16	chr7:39795400-39833400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:39795800-39811400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:39798000-39807200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:39798000-39811800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:39798200-39808200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:39798200-39820800	Weak transcription	Esophagus	oesophagus
22	chr7:39798200-39831000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:39798400-39807200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:39798400-39810200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:39798400-39830800	Weak transcription	Fetal Intestine Small	intestine
26	chr7:39798600-39807200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:39799000-39821200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:39799800-39820400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:39801600-39807200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:39801600-39810800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:39801600-39820800	Weak transcription	Placenta	Placenta
32	chr7:39801600-39831600	Weak transcription	Gastric	stomach
33	chr7:39801600-39833600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:39801800-39831000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr7:39801800-39831400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:39802000-39830800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:39802000-39835200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:39802200-39812000	Weak transcription	Fetal Intestine Large	intestine
39	chr7:39802400-39805000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:39802600-39807000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:39802600-39807000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:39802600-39812400	Weak transcription	NH-A	brain
43	chr7:39802600-39820200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:39802600-39821200	Weak transcription	Adipose Nuclei	Adipose
45	chr7:39802600-39833000	Weak transcription	Dnd41	blood
46	chr7:39802800-39807000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:39802800-39812400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr7:39802800-39830800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:39802800-39835000	Weak transcription	Brain Hippocampus Middle	brain
50	chr7:39803000-39807000	Weak transcription	Thymus	Thymus

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