Variant report

Variant	nsv1011569
Chromosome Location	chr2:34238969-34318402
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	chr2:34282612-34282876	A549	lung:	n/a	n/a
2	CEBPB	chr2:34315236-34315504	HepG2	liver:	n/a	chr2:34315355-34315366
3	CEBPB	chr2:34292173-34292361	HepG2	liver:	n/a	chr2:34292232-34292243
4	CEBPB	chr2:34282589-34282874	HepG2	liver:	n/a	n/a
5	CEBPB	chr2:34242505-34242705	HepG2	liver:	n/a	n/a
6	CTCF	chr2:34240810-34240879	Lung_OC	lung:	n/a	n/a
7	CTCF	chr2:34312037-34312114	GM20000	blood:	n/a	n/a
8	CTCF	chr2:34277080-34277230	RPTEC	kidney:	n/a	n/a
9	CTCF	chr2:34258660-34258810	NHLF	lung:	n/a	n/a
10	CTCF	chr2:34302050-34302086	K562	blood:	n/a	n/a
11	E2F4	chr2:34289805-34290093	MCF10A-Er-Src	breast:	n/a	n/a
12	EBF1	chr2:34291109-34291397	GM12878	blood:	n/a	n/a
13	EP300	chr2:34250238-34250660	T-47D	breast:	n/a	chr2:34250434-34250443 chr2:34250438-34250454
14	EP300	chr2:34250232-34250629	T-47D	breast:	n/a	chr2:34250434-34250443 chr2:34250438-34250454
15	EP300	chr2:34267505-34267860	T-47D	breast:	n/a	n/a
16	EP300	chr2:34256092-34256680	T-47D	breast:	n/a	chr2:34256144-34256153 chr2:34256211-34256225
17	EP300	chr2:34256227-34256571	T-47D	breast:	n/a	n/a
18	ESR1	chr2:34267539-34267867	T-47D	breast:	n/a	n/a
19	FOXA1	chr2:34267493-34267675	T-47D	breast:	n/a	n/a
20	FOXA1	chr2:34250298-34250559	T-47D	breast:	n/a	n/a
21	FOXA1	chr2:34250624-34251027	T-47D	breast:	n/a	chr2:34250636-34250648
22	FOXA1	chr2:34256156-34256553	T-47D	breast:	n/a	n/a
23	FOXA1	chr2:34250705-34250936	T-47D	breast:	n/a	n/a
24	FOXA1	chr2:34256230-34256597	T-47D	breast:	n/a	n/a
25	FOXP2	chr2:34250262-34250553	SK-N-MC	brain:	n/a	n/a
26	GATA2	chr2:34250281-34250627	SH-SY5Y	brain:	n/a	chr2:34250400-34250407 chr2:34250537-34250547 chr2:34250561-34250572
27	GATA3	chr2:34267452-34267789	T-47D	breast:	n/a	n/a
28	GATA3	chr2:34250211-34250744	MCF-7	breast:	n/a	chr2:34250400-34250407 chr2:34250537-34250547 chr2:34250561-34250572
29	GATA3	chr2:34250248-34250648	T-47D	breast:	n/a	chr2:34250400-34250407 chr2:34250537-34250547 chr2:34250561-34250572
30	GATA3	chr2:34250280-34250590	MCF-7	breast:	n/a	chr2:34250400-34250407 chr2:34250537-34250547 chr2:34250561-34250572
31	GATA3	chr2:34260889-34261132	SH-SY5Y	brain:	n/a	n/a
32	GATA3	chr2:34256189-34256607	T-47D	breast:	n/a	n/a
33	GATA3	chr2:34250503-34250669	SH-SY5Y	brain:	n/a	chr2:34250537-34250547 chr2:34250561-34250572
34	GATA3	chr2:34256204-34256614	T-47D	breast:	n/a	n/a
35	GATA3	chr2:34250229-34250668	T-47D	breast:	n/a	chr2:34250400-34250407 chr2:34250537-34250547 chr2:34250561-34250572
36	HDAC2	chr2:34250276-34250633	MCF-7	breast:	n/a	chr2:34250558-34250572 chr2:34250534-34250548
37	JUN	chr2:34267121-34267321	K562	blood:	n/a	n/a
38	JUN	chr2:34282669-34282870	HepG2	liver:	n/a	chr2:34282729-34282742
39	JUN	chr2:34292140-34292339	HepG2	liver:	n/a	chr2:34292218-34292231 chr2:34292196-34292209 chr2:34292233-34292246
40	JUND	chr2:34315323-34315423	HepG2	liver:	n/a	n/a
41	JUND	chr2:34292176-34292349	HepG2	liver:	n/a	n/a
42	MAFF	chr2:34254333-34254370	K562	blood:	n/a	n/a
43	MAFF	chr2:34292229-34292356	HepG2	liver:	n/a	n/a
44	MAFF	chr2:34284189-34284438	HepG2	liver:	n/a	n/a
45	MAFF	chr2:34254174-34254506	HepG2	liver:	n/a	chr2:34254320-34254338
46	MAFK	chr2:34292222-34292413	HepG2	liver:	n/a	chr2:34292274-34292288 chr2:34292267-34292284
47	MAFK	chr2:34253522-34253752	HepG2	liver:	n/a	n/a
48	MAFK	chr2:34284151-34284332	IMR90	lung:	n/a	n/a
49	MAFK	chr2:34283943-34284451	HepG2	liver:	n/a	chr2:34283969-34283980 chr2:34283970-34283981 chr2:34283968-34283982 chr2:34283969-34283980
50	MAFK	chr2:34284166-34284362	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:20811148..20811932-chr2:34244925..34245925,2	MCF-7	breast:
2	chr2:34253322..34256129-chr2:34261257..34263423,2	K562	blood:
3	chr14:20810431..20812269-chr2:34245445..34246945,2	MCF-7	breast:
4	chr2:34253322..34256129-chr2:34261257..34263423,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASGRP3-2	chr2:34288818-34293939	NONHSAT070031
2	lnc-RASGRP3-1	chr2:34286086-34286114	ENSG00000203386
3	lnc-RASGRP3-2	chr2:34292293-34292370	XLOC_001422
4	lnc-RASGRP3-2	chr2:34294166-34294617	XLOC_001422
5	lnc-RASGRP3-2	chr2:34293281-34293347	XLOC_001422
6	lnc-RASGRP3-2	chr2:34284362-34284586	NONHSAT070031
7	lnc-RASGRP3-1	chr2:34285817-34285994	ENSG00000203386

Variant related genes	Relation type
ENSG00000237790	TF binding region
ENSG00000259001	chromatin interactions
ENSG00000129484	chromatin interactions

Extended variants
information (count: 1278 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:1278 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2162008	chr2:34238969-34238970	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs116202161	chr2:34239033-34239034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs561834865	chr2:34239053-34239054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs189787247	chr2:34239076-34239077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs79665705	chr2:34239103-34239104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs111668292	chr2:34239124-34239125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs79943993	chr2:34239137-34239138	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs11687310	chr2:34239162-34239163	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs181307003	chr2:34239192-34239193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs535660065	chr2:34239222-34239223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs147521546	chr2:34239285-34239286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs140095006	chr2:34239302-34239303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs537145336	chr2:34239329-34239330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs186927416	chr2:34239334-34239335	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs576814647	chr2:34239355-34239356	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs546209949	chr2:34239436-34239437	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs565386945	chr2:34239468-34239469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs540572618	chr2:34239475-34239476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs938028	chr2:34239484-34239485	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs573733303	chr2:34239510-34239511	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs188852697	chr2:34239533-34239534	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs573422587	chr2:34239565-34239566	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs938027	chr2:34239598-34239599	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs145505623	chr2:34239611-34239612	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs116749164	chr2:34239623-34239624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs544315085	chr2:34239716-34239717	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs562569999	chr2:34239721-34239722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs115489271	chr2:34239741-34239742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs532935449	chr2:34239760-34239761	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs371922937	chr2:34239765-34239766	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs546250057	chr2:34239783-34239784	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs147751155	chr2:34239792-34239793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs529130566	chr2:34239814-34239815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs73926831	chr2:34239817-34239818	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs61286494	chr2:34239855-34239856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs149675871	chr2:34239903-34239904	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs145459144	chr2:34239904-34239905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs186334623	chr2:34239987-34239988	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs539839101	chr2:34239994-34239995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs72871453	chr2:34240008-34240009	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs573482910	chr2:34240047-34240048	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs534976844	chr2:34240081-34240082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs542153532	chr2:34240096-34240097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs556034738	chr2:34240160-34240161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs575890927	chr2:34240214-34240215	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs544351373	chr2:34240254-34240255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs190739862	chr2:34240277-34240278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs13028621	chr2:34240285-34240286	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs540228514	chr2:34240322-34240323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs559890913	chr2:34240327-34240328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Breast cancer	21364760	CNVD
Wilms tumour	21544195	CNVD
Non-small cell lung cancer	18927303	CNVD
Hereditary gingival fibromatosis	19633868	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
Autism	22495309	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:34238200-34240600	Weak transcription	Fetal Kidney	kidney
2	chr2:34240600-34240800	ZNF genes & repeats	Fetal Kidney	kidney
3	chr2:34243000-34248800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:34248800-34249200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:34249400-34250200	Weak transcription	Left Ventricle	heart
6	chr2:34249600-34250600	Enhancers	Stomach Smooth Muscle	stomach
7	chr2:34249800-34250600	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr2:34249800-34250600	Enhancers	Fetal Stomach	stomach
9	chr2:34250200-34250600	Enhancers	Colon Smooth Muscle	Colon
10	chr2:34250400-34251000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr2:34250400-34251000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr2:34250600-34255400	Weak transcription	Fetal Stomach	stomach
13	chr2:34250600-34255800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:34250600-34256000	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:34250600-34256200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:34255200-34256400	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:34255400-34255800	Enhancers	Fetal Stomach	stomach
18	chr2:34255600-34257000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:34255600-34257000	Enhancers	Fetal Heart	heart
20	chr2:34255800-34256000	Weak transcription	Fetal Stomach	stomach
21	chr2:34255800-34257000	Enhancers	Stomach Smooth Muscle	stomach
22	chr2:34256000-34256400	Enhancers	Fetal Stomach	stomach
23	chr2:34256000-34256800	Enhancers	Colon Smooth Muscle	Colon
24	chr2:34256200-34256800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr2:34262000-34262800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:34262200-34263200	Enhancers	Fetal Lung	lung
27	chr2:34270400-34270600	Enhancers	Brain Substantia Nigra	brain
28	chr2:34275000-34276000	Enhancers	Fetal Heart	heart
29	chr2:34284600-34285200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:34293000-34293200	Enhancers	Brain Hippocampus Middle	brain
31	chr2:34293000-34293600	Enhancers	Brain Substantia Nigra	brain
32	chr2:34293400-34294800	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:34293600-34295000	Weak transcription	Brain Substantia Nigra	brain
34	chr2:34294200-34294600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:34294200-34295200	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:34294200-34295800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:34294400-34294800	Enhancers	Brain Anterior Caudate	brain
38	chr2:34294600-34296200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:34294800-34295000	Enhancers	Brain Hippocampus Middle	brain
40	chr2:34295000-34295400	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:34295000-34295400	Enhancers	Brain Substantia Nigra	brain
42	chr2:34295200-34295400	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr2:34295400-34296200	Weak transcription	Brain Substantia Nigra	brain
44	chr2:34295400-34296400	Active TSS	Brain Cingulate Gyrus	brain
45	chr2:34295400-34296400	Enhancers	Brain Hippocampus Middle	brain
46	chr2:34296200-34296600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr2:34296200-34296600	ZNF genes & repeats	Brain Substantia Nigra	brain
48	chr2:34305800-34306400	Enhancers	Fetal Intestine Large	intestine

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