Variant report

Variant	esv16878
Chromosome Location	chr1:220495388-220499568
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	BHLHE40	chr1:220495373-220495390	K562	blood:	n/a	n/a
2	CTCF	chr1:220495340-220495490	Caco-2	colon:	n/a	n/a
3	CTCF	chr1:220495320-220495470	GM12864	blood:	n/a	n/a
4	CTCF	chr1:220495255-220495393	HepG2	liver:	n/a	n/a
5	CTCF	chr1:220495250-220495451	MCF-7	breast:	n/a	n/a
6	CTCF	chr1:220495260-220495410	K562	blood:	n/a	n/a
7	CTCF	chr1:220495143-220495598	K562	blood:	n/a	n/a
8	CTCF	chr1:220495234-220495398	GM12878	blood:	n/a	n/a
9	CTCF	chr1:220495154-220495540	MCF-7	breast:	n/a	n/a
10	CTCF	chr1:220495360-220495510	MCF-7	breast:	n/a	n/a
11	CTCF	chr1:220495260-220495424	K562	blood:	n/a	n/a
12	CTCF	chr1:220495258-220495435	MCF-7	breast:	n/a	n/a
13	CTCF	chr1:220495300-220495450	HepG2	liver:	n/a	n/a
14	CTCF	chr1:220495330-220495407	GM12892	blood:	n/a	n/a
15	CTCF	chr1:220495261-220495416	MCF-7	breast:	n/a	n/a
16	CTCF	chr1:220495280-220495430	WERI-Rb-1	eye:	n/a	n/a
17	CTCF	chr1:220495256-220495459	MCF-7	breast:	n/a	n/a
18	CTCF	chr1:220495214-220495489	K562	blood:	n/a	n/a
19	CTCF	chr1:220495279-220495403	MCF-7	breast:	n/a	n/a
20	CTCF	chr1:220495269-220495428	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr1:220495169-220495527	K562	blood:	n/a	n/a
22	E2F4	chr1:220498678-220498745	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr1:220498781-220499384	MCF10A-Er-Src	breast:	n/a	chr1:220499123-220499131 chr1:220499123-220499131 chr1:220499124-220499131
24	FOS	chr1:220498730-220499422	MCF10A-Er-Src	breast:	n/a	chr1:220499123-220499131 chr1:220499123-220499131 chr1:220499124-220499131
25	FOS	chr1:220498873-220499360	MCF10A-Er-Src	breast:	n/a	chr1:220499123-220499131 chr1:220499123-220499131 chr1:220499124-220499131
26	FOS	chr1:220499046-220499256	MCF10A-Er-Src	breast:	n/a	chr1:220499123-220499131 chr1:220499123-220499131 chr1:220499124-220499131
27	HCFC1	chr1:220495220-220495395	K562	blood:	n/a	n/a
28	JUND	chr1:220495346-220495396	K562	blood:	n/a	n/a
29	MAZ	chr1:220495198-220495470	K562	blood:	n/a	n/a
30	MYC	chr1:220499039-220499382	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr1:220495340-220495410	K562	blood:	n/a	n/a
32	POLR2A	chr1:220498450-220499269	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr1:220498567-220498903	Raji	blood:	n/a	n/a
34	POLR2A	chr1:220498335-220498878	GM12891	blood:	n/a	n/a
35	POLR2A	chr1:220498597-220498870	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:220498336-220498952	GM12891	blood:	n/a	n/a
37	POLR2A	chr1:220498684-220498918	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr1:220495237-220495431	K562	blood:	n/a	n/a
39	RAD21	chr1:220495109-220495507	H1-hESC	embryonic stem cell:	n/a	chr1:220495229-220495243
40	RAD21	chr1:220495213-220495410	Hela-S3	cervix:	n/a	chr1:220495229-220495243
41	RAD21	chr1:220495116-220495582	MCF-7	breast:	n/a	chr1:220495229-220495243
42	RAD21	chr1:220495136-220495553	MCF-7	breast:	n/a	chr1:220495229-220495243
43	RAD21	chr1:220495240-220495402	K562	blood:	n/a	n/a
44	RUNX3	chr1:220498603-220498938	GM12878	blood:	n/a	n/a
45	RUNX3	chr1:220498576-220498942	GM12878	blood:	n/a	n/a
46	SMC3	chr1:220495236-220495413	K562	blood:	n/a	n/a
47	SPI1	chr1:220498698-220498907	GM12891	blood:	n/a	n/a
48	STAT3	chr1:220498749-220499495	MCF10A-Er-Src	breast:	n/a	chr1:220499273-220499284 chr1:220499166-220499174 chr1:220499164-220499175
49	STAT3	chr1:220499163-220499235	MCF10A-Er-Src	breast:	n/a	chr1:220499166-220499174 chr1:220499164-220499175
50	STAT3	chr1:220498780-220499428	MCF10A-Er-Src	breast:	n/a	chr1:220499273-220499284 chr1:220499166-220499174 chr1:220499164-220499175

No.	Distal block	Cell Line	Cell type
1	chr1:220469373..220470129-chr1:220494958..220495790,3	MCF-7	breast:
2	chr1:220491693..220493296-chr1:220495769..220497470,2	K562	blood:
3	chr1:220490409..220493296-chr1:220495769..220497672,3	K562	blood:
4	chr1:220492579..220494999-chr1:220497676..220499408,2	MCF-7	breast:
5	chr1:220469913..220472006-chr1:220498061..220500308,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232883	TF binding region
ENSG00000232883	chromatin interactions

Extended variants
information (count: 203 )
Associated
traits (count: 95 )

Variant overlapped rSNPs/rCNVs (count:203 , 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	rs2175480	chr1:220495396-220495397	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs149985747	chr1:220495409-220495410	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs530303218	chr1:220495415-220495416	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs546894807	chr1:220495424-220495425	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs566684987	chr1:220495430-220495431	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs538838314	chr1:220495440-220495441	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs558774804	chr1:220495451-220495452	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs568988477	chr1:220495478-220495479	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs185159731	chr1:220495510-220495511	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs554631247	chr1:220495511-220495512	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs189892141	chr1:220495515-220495516	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs145229399	chr1:220495546-220495547	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs11589736	chr1:220495572-220495573	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs149172489	chr1:220495575-220495576	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs530740323	chr1:220495596-220495597	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs546015768	chr1:220495598-220495599	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs562698062	chr1:220495620-220495621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs531276750	chr1:220495749-220495750	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs144807308	chr1:220495779-220495780	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs561481379	chr1:220495786-220495787	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs368446409	chr1:220495789-220495790	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs6541134	chr1:220495808-220495809	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs560412412	chr1:220495809-220495810	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs532695954	chr1:220495834-220495835	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs552335474	chr1:220495930-220495931	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs569448927	chr1:220495946-220495947	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs575643902	chr1:220495982-220495983	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs548665661	chr1:220495983-220495984	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs568320002	chr1:220495984-220495985	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs56040283	chr1:220495999-220496000	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs554252707	chr1:220496021-220496022	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs147941229	chr1:220496069-220496070	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs79959303	chr1:220496075-220496076	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs528183356	chr1:220496100-220496101	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs114472416	chr1:220496101-220496102	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs576192184	chr1:220496132-220496133	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs6541135	chr1:220496140-220496141	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs6541136	chr1:220496150-220496151	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs560970455	chr1:220496152-220496153	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs6541137	chr1:220496232-220496233	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs540603778	chr1:220496264-220496265	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs141857108	chr1:220496343-220496344	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs6673482	chr1:220496379-220496380	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs569171450	chr1:220496394-220496395	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs6682177	chr1:220496424-220496425	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs552472609	chr1:220496448-220496449	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs531759481	chr1:220496454-220496455	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs147102560	chr1:220496456-220496457	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs17007446	chr1:220496472-220496473	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs151119637	chr1:220496476-220496477	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:95)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Multiple myeloma	16461302	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Holoprosencephaly	19184110	CNVD
Breast cancer	21069454	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Acute myeloid leukemia	17268525	CNVD
Lung cancer	16740712	CNVD
Renal cell carcinoma	18765545	CNVD
Basal cell lymphoma	17053054	CNVD
Developmental delay	21147756	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Autism	14699429	CNVD
Breast cancer	21364760	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Tetralogy of Fallot	22912587	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220487400-220495400	Weak transcription	Right Atrium	heart
2	chr1:220493000-220499600	Weak transcription	Fetal Heart	heart
3	chr1:220495000-220495600	Enhancers	GM12878-XiMat	blood
4	chr1:220495600-220495800	Weak transcription	Right Atrium	heart
5	chr1:220495600-220498800	Weak transcription	GM12878-XiMat	blood
6	chr1:220498400-220498800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:220498400-220498800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:220498400-220499000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:220498400-220499000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:220498400-220500200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:220498800-220499000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:220498800-220499000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:220498800-220499000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:220498800-220499000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:220498800-220499200	Enhancers	Esophagus	oesophagus
16	chr1:220498800-220500000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:220498800-220500000	Enhancers	HSMMtube	muscle
18	chr1:220498800-220500200	Enhancers	GM12878-XiMat	blood
19	chr1:220498800-220503000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:220499000-220500000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:220499000-220500200	Enhancers	NH-A	brain
22	chr1:220499000-220501600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:220499000-220502600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:220499000-220509400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:220499200-220500000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr1:220499200-220500600	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links