Variant report

Variant	nsv585744
Chromosome Location	chr20:24647725-24685440
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	chr20:24675731-24676542	MCF-7	breast:	n/a	chr20:24676333-24676344 chr20:24676332-24676349 chr20:24676334-24676345 chr20:24676333-24676346 chr20:24675893-24675906 chr20:24676335-24676344
2	CEBPB	chr20:24654123-24654740	IMR90	lung:	n/a	chr20:24654273-24654286
3	CEBPB	chr20:24676162-24676507	A549	lung:	n/a	chr20:24676333-24676344 chr20:24676332-24676349 chr20:24676334-24676345 chr20:24676333-24676346 chr20:24676335-24676344
4	CEBPB	chr20:24676202-24676506	IMR90	lung:	n/a	chr20:24676333-24676344 chr20:24676332-24676349 chr20:24676334-24676345 chr20:24676333-24676346 chr20:24676335-24676344
5	CEBPB	chr20:24676194-24676523	HepG2	liver:	n/a	chr20:24676333-24676344 chr20:24676332-24676349 chr20:24676334-24676345 chr20:24676333-24676346 chr20:24676335-24676344
6	CEBPB	chr20:24671540-24671663	HepG2	liver:	n/a	n/a
7	CEBPB	chr20:24654325-24654708	A549	lung:	n/a	n/a
8	CEBPB	chr20:24654216-24654750	A549	lung:	n/a	chr20:24654273-24654286
9	CTCF	chr20:24658433-24658502	MCF-7	breast:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
10	CTCF	chr20:24666100-24666250	BE2_C	brain:	n/a	n/a
11	CTCF	chr20:24658446-24658492	MCF-7	breast:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
12	CTCF	chr20:24653800-24653950	HA-sp	spinal cord:	n/a	n/a
13	CTCF	chr20:24666040-24666190	GM12872	blood:	n/a	n/a
14	CTCF	chr20:24666169-24666257	NHEK	skin:	n/a	n/a
15	CTCF	chr20:24653500-24653650	HCPEpiC	choroid plexus:	n/a	n/a
16	CTCF	chr20:24665885-24666334	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr20:24658360-24658510	GM12865	blood:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
18	CTCF	chr20:24653860-24654010	HCPEpiC	choroid plexus:	n/a	n/a
19	CTCF	chr20:24666159-24666243	K562	blood:	n/a	n/a
20	CTCF	chr20:24666055-24666057	MCF-7	breast:	n/a	n/a
21	CTCF	chr20:24654420-24654570	HMF	breast:	n/a	n/a
22	CTCF	chr20:24669273-24669334	Lung_OC	lung:	n/a	n/a
23	CTCF	chr20:24653860-24654010	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr20:24658254-24658591	H1-hESC	embryonic stem cell:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
25	CTCF	chr20:24675987-24676043	MCF-7	breast:	n/a	n/a
26	CTCF	chr20:24666151-24666175	GM12878	blood:	n/a	n/a
27	CTCF	chr20:24665960-24666110	HEK293	kidney:	n/a	n/a
28	CTCF	chr20:24658416-24658534	MCF-7	breast:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
29	CTCF	chr20:24665980-24666130	HRE	kidney:	n/a	n/a
30	CTCF	chr20:24658404-24658515	MCF-7	breast:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
31	CTCF	chr20:24665950-24666365	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr20:24665980-24666130	WERI-Rb-1	eye:	n/a	n/a
33	CTCF	chr20:24666020-24666170	MCF-7	breast:	n/a	n/a
34	CTCF	chr20:24666000-24666150	HRE	kidney:	n/a	n/a
35	CTCF	chr20:24658400-24658550	HPF	lung:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
36	CTCF	chr20:24665988-24666288	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr20:24658420-24658531	MCF-7	breast:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
38	CTCF	chr20:24666040-24666190	HMEC	breast:	n/a	n/a
39	CTCF	chr20:24658416-24658522	GM12892	blood:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
40	CTCF	chr20:24666060-24666210	WERI-Rb-1	eye:	n/a	n/a
41	CTCF	chr20:24653060-24653210	HCPEpiC	choroid plexus:	n/a	n/a
42	CTCF	chr20:24658402-24658555	H1-hESC	embryonic stem cell:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
43	CTCF	chr20:24658440-24658590	GM06990	blood:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
44	CTCF	chr20:24654446-24654601	NHEK	skin:	n/a	n/a
45	CTCF	chr20:24665940-24666090	HepG2	liver:	n/a	n/a
46	CTCF	chr20:24658360-24658510	WERI-Rb-1	eye:	n/a	chr20:24658454-24658475 chr20:24658459-24658477
47	CTCF	chr20:24653160-24653310	BJ	skin:	n/a	n/a
48	EBF1	chr20:24656921-24657149	GM12878	blood:	n/a	chr20:24657005-24657016 chr20:24657007-24657017 chr20:24657007-24657016 chr20:24657005-24657018
49	EP300	chr20:24653290-24654077	SK-N-SH	brain:	n/a	n/a
50	EP300	chr20:24659220-24659744	MCF-7	breast:	n/a	chr20:24659310-24659326

No.	Distal block	Cell Line	Cell type
1	chr20:24671407..24673133-chr20:24673157..24675510,2	K562	blood:
2	chr20:24651840..24653392-chr20:24727209..24728729,2	MCF-7	breast:
3	chr20:24629448..24631960-chr20:24674530..24677062,2	MCF-7	breast:
4	chr20:24645110..24646856-chr20:24648654..24651485,2	MCF-7	breast:
5	chr20:24671696..24673797-chr20:24673883..24676356,3	MCF-7	breast:
6	chr20:24645518..24647041-chr20:24652515..24654778,2	MCF-7	breast:
7	chr20:24616131..24617827-chr20:24647064..24649863,2	MCF-7	breast:
8	chr20:24629731..24632578-chr20:24657556..24659618,3	MCF-7	breast:
9	chr20:24654225..24656073-chr20:24661737..24664471,2	MCF-7	breast:
10	chr20:24671696..24673797-chr20:24673883..24676356,3	MCF-7	breast:
11	chr20:24671407..24673133-chr20:24673157..24675510,2	K562	blood:
12	chr20:24631399..24634097-chr20:24646074..24647990,2	MCF-7	breast:
13	chr20:24654225..24656073-chr20:24661737..24664471,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNDIG1-1	chr20:24660183-24660300	XLOC_013498
2	lnc-SYNDIG1-1	chr20:24660941-24661627	XLOC_013498

Variant related genes	Relation type
ENSG00000231015	TF binding region

Extended variants
information (count: 1728 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:1728 , 50 per page) page: 1 2 3 4 5 6 7 ... 35

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12624459	chr20:24647725-24647726	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs146104698	chr20:24647727-24647728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs372013929	chr20:24647731-24647732	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs190617699	chr20:24647761-24647762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs560646847	chr20:24647897-24647898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs761439	chr20:24647918-24647919	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs146854395	chr20:24647929-24647930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs529264201	chr20:24647941-24647942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs539825719	chr20:24647942-24647943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs559743794	chr20:24647968-24647969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs2006215	chr20:24647987-24647988	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs140645914	chr20:24647994-24647995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs201749041	chr20:24647995-24647996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs2006216	chr20:24648007-24648008	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs548410048	chr20:24648039-24648040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs386813496	chr20:24648048-24648049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs138301240	chr20:24648050-24648051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs553377318	chr20:24648092-24648093	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs567048052	chr20:24648108-24648109	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs7263380	chr20:24648157-24648158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs569719747	chr20:24648160-24648161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs3085110	chr20:24648181-24648182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs527929761	chr20:24648217-24648218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs6138346	chr20:24648230-24648231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs2387080	chr20:24648255-24648256	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs118180740	chr20:24648259-24648260	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs575940579	chr20:24648261-24648262	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs6138347	chr20:24648272-24648273	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs544470117	chr20:24648273-24648274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs182447617	chr20:24648285-24648286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs6049840	chr20:24648303-24648304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs375465683	chr20:24648304-24648305	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs6049841	chr20:24648410-24648411	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs186144831	chr20:24648454-24648455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs190795253	chr20:24648501-24648502	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs182994845	chr20:24648505-24648506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs148836244	chr20:24648513-24648514	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs187325831	chr20:24648626-24648627	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs77148450	chr20:24648637-24648638	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs73100772	chr20:24648665-24648666	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs73100774	chr20:24648677-24648678	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs190285631	chr20:24648735-24648736	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs530185026	chr20:24648748-24648749	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs6049842	chr20:24648764-24648765	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs566826360	chr20:24648775-24648776	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs538654738	chr20:24648833-24648834	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs143439960	chr20:24648857-24648858	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs73100778	chr20:24648927-24648928	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs374445841	chr20:24648941-24648942	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs538558092	chr20:24648983-24648984	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:269 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24634600-24648800	Weak transcription	Gastric	stomach
2	chr20:24639000-24650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:24639200-24648600	Weak transcription	Spleen	Spleen
4	chr20:24641200-24654000	Weak transcription	Aorta	Aorta
5	chr20:24641400-24649400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:24641800-24649800	Weak transcription	Right Ventricle	heart
7	chr20:24643400-24649400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:24643400-24661400	Weak transcription	Right Atrium	heart
9	chr20:24645800-24657200	Weak transcription	Brain Anterior Caudate	brain
10	chr20:24646200-24648600	Weak transcription	Fetal Brain Male	brain
11	chr20:24646200-24649400	Weak transcription	Fetal Muscle Leg	muscle
12	chr20:24646400-24650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:24646400-24657200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr20:24646600-24657400	Weak transcription	Brain Substantia Nigra	brain
15	chr20:24646800-24657200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr20:24646800-24657400	Weak transcription	Brain Angular Gyrus	brain
17	chr20:24647600-24653800	Weak transcription	Brain Hippocampus Middle	brain
18	chr20:24648600-24649400	Enhancers	Spleen	Spleen
19	chr20:24648800-24649000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
20	chr20:24648800-24649000	Enhancers	Gastric	stomach
21	chr20:24649000-24657200	Weak transcription	Gastric	stomach
22	chr20:24649400-24649600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:24649400-24649800	Flanking Active TSS	Spleen	Spleen
24	chr20:24649400-24655600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:24649600-24650000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr20:24649800-24650000	Enhancers	Spleen	Spleen
27	chr20:24650000-24650200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr20:24650000-24650200	Flanking Active TSS	Spleen	Spleen
29	chr20:24650000-24650600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:24650200-24650800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:24650200-24650800	Enhancers	Spleen	Spleen
32	chr20:24650200-24651600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr20:24650400-24650600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr20:24650400-24651200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:24650600-24650800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr20:24650600-24653200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:24650600-24655000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:24650800-24651000	Enhancers	HSMMtube	muscle
39	chr20:24650800-24651800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr20:24650800-24652400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr20:24650800-24652800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr20:24650800-24652800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr20:24651200-24652600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:24651400-24652600	Weak transcription	HSMMtube	muscle
45	chr20:24651600-24651800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr20:24651600-24653800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:24651800-24659000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr20:24652200-24655000	Enhancers	NHLF	lung
49	chr20:24652400-24654600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr20:24652400-24654800	Enhancers	HSMM	muscle

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