Variant report

Variant	nsv1064465
Chromosome Location	chr20:52643155-52658639
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr20:52652599-52652817	A549	lung:	n/a	chr20:52652797-52652809
2	CTCF	chr20:52656980-52657130	NHDF-neo	bronchial:	n/a	n/a
3	CTCF	chr20:52643380-52643530	HL-60	blood:	n/a	n/a
4	CTCF	chr20:52644932-52644961	ProgFib	skin:	n/a	n/a
5	CTCF	chr20:52644962-52644976	ProgFib	skin:	n/a	n/a
6	CTCF	chr20:52649892-52649926	Lung_OC	lung:	n/a	n/a
7	FOS	chr20:52642967-52643197	MCF10A-Er-Src	breast:	n/a	chr20:52643036-52643045 chr20:52643034-52643046 chr20:52643035-52643044 chr20:52643035-52643045
8	GATA3	chr20:52646629-52646974	SH-SY5Y	brain:	n/a	n/a
9	GTF2F1	chr20:52655601-52655670	K562	blood:	n/a	n/a
10	JUND	chr20:52642962-52643219	HepG2	liver:	n/a	chr20:52643036-52643045 chr20:52643034-52643046 chr20:52643035-52643044 chr20:52643034-52643045 chr20:52643035-52643045
11	MYC	chr20:52644910-52644973	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr20:52655714-52655734	K562	blood:	n/a	n/a
13	POLR2A	chr20:52645224-52645292	ProgFib	skin:	n/a	n/a
14	POLR2A	chr20:52644598-52644700	ProgFib	skin:	n/a	n/a
15	POLR2A	chr20:52644891-52645058	A549	lung:	n/a	n/a
16	POLR2A	chr20:52646455-52646601	ProgFib	skin:	n/a	n/a
17	POLR2A	chr20:52644898-52645206	ProgFib	skin:	n/a	n/a
18	POLR2A	chr20:52644817-52644821	ProgFib	skin:	n/a	n/a
19	POLR2A	chr20:52656922-52656928	ProgFib	skin:	n/a	n/a
20	RCOR1	chr20:52654150-52654334	K562	blood:	n/a	n/a
21	RCOR1	chr20:52654183-52654358	K562	blood:	n/a	n/a
22	SPI1	chr20:52657027-52657212	K562	blood:	n/a	n/a
23	STAT3	chr20:52643042-52643161	MCF10A-Er-Src	breast:	n/a	chr20:52643087-52643098 chr20:52643089-52643097
24	STAT3	chr20:52643024-52643161	MCF10A-Er-Src	breast:	n/a	chr20:52643087-52643098 chr20:52643036-52643045 chr20:52643089-52643097
25	USF2	chr20:52644979-52644984	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF384	chr20:52658357-52658546	K562	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52640367..52641889-chr20:52645625..52647973,2	K562	blood:
2	chr20:52646516..52648390-chr3:62045905..62047422,2	MCF-7	breast:
3	chr20:52643210..52646138-chr20:52658422..52660423,2	K562	blood:
4	chr20:52648757..52649473-chr5:157170244..157171208,2	MCF-7	breast:
5	chr20:52626505..52628533-chr20:52652801..52654568,2	MCF-7	breast:
6	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
7	chr20:52642833..52647245-chr20:52651317..52656592,5	MCF-7	breast:
8	chr19:11025812..11027987-chr20:52653374..52655752,2	MCF-7	breast:
9	chr20:52637408..52640155-chr20:52655059..52656752,2	MCF-7	breast:
10	chr20:52647368..52649299-chr20:52654193..52656329,2	MCF-7	breast:
11	chr20:52643673..52645639-chr20:52687051..52688962,2	MCF-7	breast:
12	chr17:56707799..56710607-chr20:52642228..52644941,3	MCF-7	breast:
13	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
14	chr20:52621471..52622138-chr20:52658585..52659278,2	MCF-7	breast:
15	chr20:52645173..52647456-chr8:56684089..56685719,2	MCF-7	breast:
16	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
17	chr17:57917278..57919596-chr20:52653625..52656516,2	MCF-7	breast:
18	chr20:52647368..52649299-chr20:52654193..52656329,2	MCF-7	breast:
19	chr20:52655188..52657937-chr20:55839006..55840900,2	MCF-7	breast:
20	chr17:57915947..57917652-chr20:52646723..52649567,2	MCF-7	breast:
21	chr2:99769202..99772000-chr20:52646224..52647934,2	MCF-7	breast:
22	chr20:45987538..45989784-chr20:52646421..52648098,2	MCF-7	breast:

No data

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000199004	chromatin interactions
ENSG00000064787	chromatin interactions
ENSG00000212195	chromatin interactions
ENSG00000137574	chromatin interactions
ENSG00000135951	chromatin interactions
ENSG00000273155	chromatin interactions
ENSG00000101144	chromatin interactions
ENSG00000155858	chromatin interactions
ENSG00000167904	chromatin interactions
ENSG00000144182	chromatin interactions

Extended variants
information (count: 649 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:649 , 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	rs208384	chr20:52643155-52643156	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs184729294	chr20:52643184-52643185	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs572996037	chr20:52643188-52643189	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs79247156	chr20:52643241-52643242	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs148024360	chr20:52643245-52643246	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs570476802	chr20:52643248-52643249	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs544485047	chr20:52643254-52643255	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs187235276	chr20:52643293-52643294	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs62215569	chr20:52643303-52643304	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs574440433	chr20:52643314-52643315	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs6022923	chr20:52643316-52643317	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs540002154	chr20:52643371-52643372	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs75300730	chr20:52643378-52643379	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs141744998	chr20:52643400-52643401	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs573051829	chr20:52643403-52643404	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs546355212	chr20:52643416-52643417	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs562714965	chr20:52643427-52643428	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs531894974	chr20:52643450-52643451	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs150575958	chr20:52643473-52643474	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs192050247	chr20:52643489-52643490	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs117744509	chr20:52643494-52643495	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs184454177	chr20:52643504-52643505	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs547612437	chr20:52643520-52643521	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs570905435	chr20:52643558-52643559	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs371963553	chr20:52643563-52643564	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs3835351	chr20:52643576-52643577	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs33964882	chr20:52643577-52643578	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs189202170	chr20:52643597-52643598	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs569032835	chr20:52643608-52643609	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs376979918	chr20:52643666-52643667	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs376283409	chr20:52643684-52643685	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs554901866	chr20:52643719-52643720	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs6068755	chr20:52643753-52643754	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs158549	chr20:52643768-52643769	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs540208675	chr20:52643809-52643810	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs140618274	chr20:52643810-52643811	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs577754053	chr20:52643815-52643816	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs576894177	chr20:52643824-52643825	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs182352023	chr20:52643839-52643840	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs562750459	chr20:52643840-52643841	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs531742812	chr20:52643849-52643850	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs201122715	chr20:52643852-52643853	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs540312357	chr20:52643873-52643874	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs185739086	chr20:52643893-52643894	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs144190588	chr20:52643908-52643909	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs527715613	chr20:52643912-52643913	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs547793684	chr20:52643937-52643938	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs60589876	chr20:52643958-52643959	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs533476332	chr20:52643960-52643961	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs560189076	chr20:52643966-52643967	Weak transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Gastric cancer	17908304	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Medulloblastoma	21979893	CNVD
Urothelial carcinoma	21177765	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Colorectal cancer	21645411	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	21693616	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
colon cancer	17210682	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	22028636	CNVD
Breast cancer	21264507	CNVD
Thyroid cancer	19087340	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Colorectal cancer	19359472	CNVD
Gastric cancer	17167181	CNVD
Myeloproliferative neoplasm	19047681	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	17603634	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17133270	CNVD
Oral cancer	21386901	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Myelodysplastic syndrome	21251322	CNVD
Ductal carcinoma	22052326	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Gastric cancer	20585902	CNVD
Ductal carcinoma	18381933	CNVD
Cancer	21129771	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	20864512	CNVD
Ovarian cancer	22174824	CNVD
Lung cancer	16740712	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16620391	CNVD
Okamoto syndrome	17623483	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21785460	CNVD
Bladder cancer	21909424	CNVD
Biliary cancer	19435499	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Cervical cancer	16585170	CNVD
Ovarian cancer	20844748	CNVD
Hirschsprung''s Disease	21712996	CNVD
Breast cancer	21364760	CNVD
Breast cancer	20459607	CNVD
Gastric cancer	18160780	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52634800-52645400	Weak transcription	Fetal Lung	lung
4	chr20:52640800-52643800	Enhancers	Fetal Brain Male	brain
5	chr20:52641000-52643200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:52641000-52643400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:52641200-52644400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr20:52641400-52646000	Active TSS	Brain Anterior Caudate	brain
9	chr20:52641600-52643400	Enhancers	HSMM	muscle
10	chr20:52641600-52646000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
12	chr20:52641800-52644600	Weak transcription	Fetal Kidney	kidney
13	chr20:52641800-52646000	Active TSS	Brain Substantia Nigra	brain
14	chr20:52642000-52643200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr20:52642000-52643200	Weak transcription	Colon Smooth Muscle	Colon
16	chr20:52642200-52643400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr20:52642200-52645400	Weak transcription	Brain Germinal Matrix	brain
18	chr20:52642200-52645600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr20:52642200-52645800	Active TSS	Brain Angular Gyrus	brain
20	chr20:52642400-52643200	Enhancers	HSMMtube	muscle
21	chr20:52642400-52643400	Enhancers	NHDF-Ad	bronchial
22	chr20:52642400-52643800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:52642400-52644800	Weak transcription	Fetal Brain Female	brain
24	chr20:52642400-52646000	Active TSS	Brain Hippocampus Middle	brain
25	chr20:52642600-52645400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:52642600-52645800	Active TSS	Brain Cingulate Gyrus	brain
27	chr20:52642800-52643200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:52643000-52643600	Enhancers	Ovary	ovary
29	chr20:52643200-52643400	Enhancers	Colon Smooth Muscle	Colon
30	chr20:52643200-52643600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:52643200-52643600	Flanking Active TSS	HSMMtube	muscle
32	chr20:52643200-52645400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr20:52643200-52645600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr20:52643400-52644000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr20:52643400-52645200	Weak transcription	NHDF-Ad	bronchial
36	chr20:52643600-52645000	Active TSS	HSMMtube	muscle
37	chr20:52643800-52645000	Weak transcription	Fetal Brain Male	brain
38	chr20:52643800-52646000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr20:52644000-52644600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr20:52644200-52644800	Weak transcription	Fetal Stomach	stomach
41	chr20:52644400-52644800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr20:52644600-52644800	Enhancers	Fetal Kidney	kidney
43	chr20:52644600-52644800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
44	chr20:52644600-52645600	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr20:52644800-52645200	Genic enhancers	Fetal Stomach	stomach
46	chr20:52644800-52645200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
47	chr20:52644800-52645600	Enhancers	Fetal Brain Female	brain
48	chr20:52644800-52645600	Enhancers	Fetal Muscle Leg	muscle
49	chr20:52644800-52646000	Strong transcription	Gastric	stomach
50	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum

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