Variant report

Variant	esv3523022
Chromosome Location	chr1:152554878-152591176
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:97)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:97 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr1:152555244-152555264	K562	blood:	n/a	chr1:152555246-152555260
2	CEBPB	chr1:152569565-152569765	HepG2	liver:	n/a	n/a
3	CTCF	chr1:152558127-152558330	GM12878	blood:	n/a	n/a
4	CTCF	chr1:152558200-152558350	HRE	kidney:	n/a	n/a
5	CTCF	chr1:152558180-152558330	HCT-116	colon:	n/a	n/a
6	CTCF	chr1:152590866-152590922	GM10248	blood:	n/a	n/a
7	CTCF	chr1:152558138-152558312	Gliobla	brain:	n/a	n/a
8	CTCF	chr1:152558160-152558310	NB4	blood:	n/a	n/a
9	CTCF	chr1:152558060-152558210	RPTEC	kidney:	n/a	n/a
10	CTCF	chr1:152558140-152558290	GM12872	blood:	n/a	n/a
11	CTCF	chr1:152558140-152558290	GM12871	blood:	n/a	n/a
12	CTCF	chr1:152557900-152558050	GM12873	blood:	n/a	n/a
13	CTCF	chr1:152558060-152558210	GM12869	blood:	n/a	n/a
14	CTCF	chr1:152558180-152558330	GM12873	blood:	n/a	n/a
15	CTCF	chr1:152558140-152558290	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr1:152558166-152558316	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr1:152558158-152558309	HepG2	liver:	n/a	n/a
18	CTCF	chr1:152558160-152558310	GM12874	blood:	n/a	n/a
19	CTCF	chr1:152558120-152558270	GM12870	blood:	n/a	n/a
20	CTCF	chr1:152558200-152558350	GM12865	blood:	n/a	n/a
21	CTCF	chr1:152558100-152558250	HepG2	liver:	n/a	n/a
22	CTCF	chr1:152558140-152558290	GM12870	blood:	n/a	n/a
23	CTCF	chr1:152558174-152558291	GM20000	blood:	n/a	n/a
24	CTCF	chr1:152558180-152558330	GM12866	blood:	n/a	n/a
25	CTCF	chr1:152558120-152558270	GM12871	blood:	n/a	n/a
26	CTCF	chr1:152558180-152558330	GM12868	blood:	n/a	n/a
27	CTCF	chr1:152558187-152558309	GM10266	blood:	n/a	n/a
28	CTCF	chr1:152558140-152558290	GM12864	blood:	n/a	n/a
29	CTCF	chr1:152558280-152558430	RPTEC	kidney:	n/a	n/a
30	CTCF	chr1:152558100-152558250	GM12864	blood:	n/a	n/a
31	CTCF	chr1:152558219-152558261	GM13976	blood:	n/a	n/a
32	CTCF	chr1:152558167-152558328	K562	blood:	n/a	n/a
33	CTCF	chr1:152558178-152558296	LNCaP	prostate:	n/a	n/a
34	CTCF	chr1:152558140-152558316	NHEK	skin:	n/a	n/a
35	CTCF	chr1:152580040-152580190	GM12874	blood:	n/a	chr1:152580060-152580068
36	CTCF	chr1:152558180-152558330	HMF	breast:	n/a	n/a
37	CTCF	chr1:152558250-152558293	Kidney_OC	kidney:	n/a	n/a
38	CTCF	chr1:152558100-152558250	K562	blood:	n/a	n/a
39	CTCF	chr1:152558120-152558270	GM12867	blood:	n/a	n/a
40	CTCF	chr1:152558160-152558310	GM12873	blood:	n/a	n/a
41	CTCF	chr1:152558140-152558290	GM12874	blood:	n/a	n/a
42	CTCF	chr1:152557580-152557730	GM12872	blood:	n/a	n/a
43	CTCF	chr1:152557760-152557910	GM12864	blood:	n/a	n/a
44	CTCF	chr1:152558140-152558290	HMEC	breast:	n/a	n/a
45	CTCF	chr1:152558160-152558310	GM12865	blood:	n/a	n/a
46	CTCF	chr1:152558064-152558405	GM12878	blood:	n/a	n/a
47	CTCF	chr1:152558120-152558270	HCPEpiC	choroid plexus:	n/a	n/a
48	CTCF	chr1:152558120-152558270	GM12872	blood:	n/a	n/a
49	CTCF	chr1:152558171-152558329	GM10248	blood:	n/a	n/a
50	CTCF	chr1:152558223-152558283	GM19240	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152550535..152553138-chr1:152591146..152593497,2	K562	blood:
2	chr1:152580545..152582523-chr1:152584809..152586590,2	K562	blood:

No data

Variant related genes	Relation type
LCE3C	TF binding region
LCE3B	TF binding region
LCE3D	TF binding region
ENSG00000163202	chromatin interactions
ENSG00000187238	chromatin interactions

Extended variants
information (count: 111 )
Associated
traits (count: 120 )

Variant overlapped rSNPs/rCNVs (count:111 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs373341370	chr1:152554882-152554883	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs550635967	chr1:152554909-152554910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs192707793	chr1:152554921-152554922	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs544888140	chr1:152554990-152554991	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs4112789	chr1:152555005-152555006	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs78637623	chr1:152555006-152555007	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs537722891	chr1:152555148-152555149	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs6687303	chr1:152555157-152555158	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs477392	chr1:152555176-152555177	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs549619042	chr1:152555187-152555188	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs569437553	chr1:152555188-152555189	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs538569599	chr1:152555191-152555192	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs552078723	chr1:152555254-152555255	Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs571658521	chr1:152555302-152555303	Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs548383460	chr1:152555312-152555313	Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs369196865	chr1:152555319-152555320	Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs554090567	chr1:152555421-152555422	Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs556112415	chr1:152555644-152555645	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs199694096	chr1:152557622-152557623	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs138460838	chr1:152557702-152557703	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs193124895	chr1:152557769-152557770	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs534910658	chr1:152557794-152557795	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs149260906	chr1:152557815-152557816	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs143468253	chr1:152557884-152557885	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs375187530	chr1:152568881-152568882	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs74678552	chr1:152569573-152569574	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs548161119	chr1:152569601-152569602	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs571596495	chr1:152569620-152569621	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs534082284	chr1:152569690-152569691	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs74131807	chr1:152569693-152569694	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs567384317	chr1:152569772-152569773	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs61130905	chr1:152569842-152569843	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs555911991	chr1:152569850-152569851	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs113139072	chr1:152570001-152570002	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs545274520	chr1:152570047-152570048	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs574975725	chr1:152570053-152570054	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs367939853	chr1:152570056-152570057	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs553633974	chr1:152570057-152570058	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs73019242	chr1:152570081-152570082	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs192069597	chr1:152570082-152570083	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs539494207	chr1:152570124-152570125	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs560975072	chr1:152570133-152570134	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs557692799	chr1:152580590-152580591	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs376531442	chr1:152580603-152580604	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs572898909	chr1:152580608-152580609	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs187335548	chr1:152580639-152580640	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs540176093	chr1:152580652-152580653	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs561533624	chr1:152580653-152580654	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs371471682	chr1:152580712-152580713	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs573551640	chr1:152580718-152580719	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:120)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	21129771	CNVD
Non-small cell lung cancer	21385341	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Ewing''s sarcoma	21437220	CNVD
Liposarcoma	21253554	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Breast cancer	20409316	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Glioblastoma multiforme	21080181	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Lung cancer	18438408	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Systemic lupus erythematosus	21956041	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	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
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	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	17899364	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21611746	CNVD
Retinoblastoma	19183342	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Ewing''s sarcoma	17952124	CNVD
Osteosarcoma	17242211	CNVD
Ovarian cancer	17242211	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Schizophrenia	18990708	CNVD
Sudden cardiac death	19188705	CNVD
Plasma-cell dyscrasia	16705089	CNVD
Myeloma	17024118	CNVD
Cancer	17060936	CNVD
Multiple myeloma	16616336	CNVD
Type 2 diabetes	19141583	CNVD
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	18703704	CNVD
Breast cancer	21509527	CNVD
Bladder cancer	21909424	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Myelofibrosis	22110671	CNVD
Liver carcinoma	19366792	CNVD
Testicular germ cell tumor	18059402	CNVD
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Gastrointestinal cancer	16790693	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Glioblastoma multiforme	21138945	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152550800-152555200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:152553400-152555000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:152553400-152555000	Weak transcription	HMEC	breast
4	chr1:152553400-152555200	Weak transcription	NHEK	skin
5	chr1:152555000-152555600	Flanking Active TSS	A549	lung
6	chr1:152555000-152555600	Enhancers	HMEC	breast
7	chr1:152555000-152555800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:152555200-152555600	Enhancers	NHEK	skin
9	chr1:152555400-152555600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:152555400-152555800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:152569600-152570200	Enhancers	Liver	Liver
12	chr1:152591000-152592600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:152591000-152592600	ZNF genes & repeats	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links