Variant report

Variant	nsv1004638
Chromosome Location	chr1:152540270-152586582
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:143)
CpG islands
(count:244)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:143 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr1:152549641-152550036	GM12878	blood:	n/a	n/a
2	BACH1	chr1:152555244-152555264	K562	blood:	n/a	chr1:152555246-152555260
3	BATF	chr1:152549573-152550008	GM12878	blood:	n/a	n/a
4	BATF	chr1:152549615-152549949	GM12878	blood:	n/a	n/a
5	CEBPB	chr1:152546403-152546497	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr1:152569565-152569765	HepG2	liver:	n/a	n/a
7	CTCF	chr1:152558140-152558290	GM12864	blood:	n/a	n/a
8	CTCF	chr1:152558166-152558276	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr1:152558187-152558309	GM10266	blood:	n/a	n/a
10	CTCF	chr1:152558140-152558316	NHEK	skin:	n/a	n/a
11	CTCF	chr1:152558180-152558330	GM12866	blood:	n/a	n/a
12	CTCF	chr1:152558174-152558291	GM20000	blood:	n/a	n/a
13	CTCF	chr1:152558100-152558250	HMF	breast:	n/a	n/a
14	CTCF	chr1:152558060-152558210	RPTEC	kidney:	n/a	n/a
15	CTCF	chr1:152558185-152558296	GM13977	blood:	n/a	n/a
16	CTCF	chr1:152558100-152558250	GM12864	blood:	n/a	n/a
17	CTCF	chr1:152558180-152558330	HMF	breast:	n/a	n/a
18	CTCF	chr1:152552800-152552950	WERI-Rb-1	eye:	n/a	chr1:152552927-152552936 chr1:152552921-152552939
19	CTCF	chr1:152558120-152558270	GM12878	blood:	n/a	n/a
20	CTCF	chr1:152558180-152558330	HEEpiC	esophagus:	n/a	n/a
21	CTCF	chr1:152558219-152558261	GM13976	blood:	n/a	n/a
22	CTCF	chr1:152558201-152558277	K562	blood:	n/a	n/a
23	CTCF	chr1:152558280-152558430	RPTEC	kidney:	n/a	n/a
24	CTCF	chr1:152552840-152552990	HMEC	breast:	n/a	chr1:152552927-152552936 chr1:152552921-152552939
25	CTCF	chr1:152558060-152558210	BE2_C	brain:	n/a	n/a
26	CTCF	chr1:152558171-152558329	GM10248	blood:	n/a	n/a
27	CTCF	chr1:152557900-152558050	GM12873	blood:	n/a	n/a
28	CTCF	chr1:152558145-152558310	LNCaP	prostate:	n/a	n/a
29	CTCF	chr1:152557580-152557730	GM12872	blood:	n/a	n/a
30	CTCF	chr1:152558167-152558328	K562	blood:	n/a	n/a
31	CTCF	chr1:152580040-152580190	GM12874	blood:	n/a	chr1:152580060-152580068
32	CTCF	chr1:152558127-152558330	GM12878	blood:	n/a	n/a
33	CTCF	chr1:152558240-152558390	HCT-116	colon:	n/a	n/a
34	CTCF	chr1:152558140-152558290	GM12872	blood:	n/a	n/a
35	CTCF	chr1:152549740-152549890	GM06990	blood:	n/a	n/a
36	CTCF	chr1:152558140-152558290	AG09319	gingival:	n/a	n/a
37	CTCF	chr1:152558180-152558330	GM12868	blood:	n/a	n/a
38	CTCF	chr1:152552201-152552270	MCF-7	breast:	n/a	n/a
39	CTCF	chr1:152558120-152558270	GM12870	blood:	n/a	n/a
40	CTCF	chr1:152558223-152558283	GM19240	blood:	n/a	n/a
41	CTCF	chr1:152558250-152558293	Kidney_OC	kidney:	n/a	n/a
42	CTCF	chr1:152558060-152558210	GM12869	blood:	n/a	n/a
43	CTCF	chr1:152552800-152552950	NHEK	skin:	n/a	chr1:152552927-152552936 chr1:152552921-152552939
44	CTCF	chr1:152558178-152558296	LNCaP	prostate:	n/a	n/a
45	CTCF	chr1:152558100-152558250	K562	blood:	n/a	n/a
46	CTCF	chr1:152558180-152558330	GM12875	blood:	n/a	n/a
47	CTCF	chr1:152558140-152558290	GM12871	blood:	n/a	n/a
48	CTCF	chr1:152558180-152558330	HCT-116	colon:	n/a	n/a
49	CTCF	chr1:152558140-152558290	GM12874	blood:	n/a	n/a
50	CTCF	chr1:152558160-152558310	NB4	blood:	n/a	n/a

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:152553244-152553294	NT2-D1	testis:	n/a
2	chr1:152552175-152552225	HMEC	breast:	n/a
3	chr1:152553244-152553294	HCM	heart:	n/a
4	chr1:152552175-152552225	SK-N-SH_RA	brain:	n/a
5	chr1:152553244-152553294	HRE	kidney:	n/a
6	chr1:152553096-152553146	AG04449	skin:	fetal
7	chr1:152552494-152552544	SK-N-SH_RA	brain:	n/a
8	chr1:152553244-152553294	SK-N-SH	brain:	n/a
9	chr1:152552494-152552544	AG09319	gingival:	n/a
10	chr1:152552494-152552544	AG09309	skin:	n/a
11	chr1:152552494-152552544	T-47D	breast:	n/a
12	chr1:152552494-152552544	PrEC	prostate:	n/a
13	chr1:152552175-152552225	SK-N-MC	brain:	n/a
14	chr1:152552494-152552544	GM12892	blood:	n/a
15	chr1:152553244-152553294	SK-N-SH_RA	brain:	n/a
16	chr1:152553096-152553146	ProgFib	skin:	n/a
17	chr1:152553096-152553146	HIPEpiC	eye:	n/a
18	chr1:152552175-152552225	BE2_C	brain:	n/a
19	chr1:152552175-152552225	SKMC	muscle:	n/a
20	chr1:152553096-152553146	MCF10A-Er-Src	breast:	n/a
21	chr1:152552175-152552225	PANC-1	pancreas:	n/a
22	chr1:152552494-152552544	HCT-116	colon:	n/a
23	chr1:152553244-152553294	GM12878	blood:	n/a
24	chr1:152553244-152553294	RPTEC	kidney:	n/a
25	chr1:152552175-152552225	GM06990	blood:	n/a
26	chr1:152553244-152553294	GM12891	blood:	n/a
27	chr1:152553244-152553294	HEEpiC	esophagus:	n/a
28	chr1:152553244-152553294	AG09309	skin:	n/a
29	chr1:152553244-152553294	BJ	skin:	n/a
30	chr1:152553244-152553294	PrEC	prostate:	n/a
31	chr1:152553096-152553146	HMEC	breast:	n/a
32	chr1:152552494-152552544	NHBE	bronchial:	n/a
33	chr1:152552175-152552225	HEK293	kidney:	embryo
34	chr1:152552175-152552225	HCF	heart:	n/a
35	chr1:152552175-152552225	GM12878	blood:	n/a
36	chr1:152552175-152552225	AG04449	skin:	fetal
37	chr1:152553096-152553146	SAEC	small airway:	n/a
38	chr1:152552175-152552225	NT2-D1	testis:	n/a
39	chr1:152553096-152553146	HRPEpiC	eye:	n/a
40	chr1:152552494-152552544	BE2_C	brain:	n/a
41	chr1:152553244-152553294	SK-N-MC	brain:	n/a
42	chr1:152552494-152552544	PANC-1	pancreas:	n/a
43	chr1:152553244-152553294	Hela-S3	cervix:	n/a
44	chr1:152552494-152552544	AG04450	lung:	fetal
45	chr1:152553096-152553146	CMK	blood:	n/a
46	chr1:152553244-152553294	ECC-1	luminal epithelium:	n/a
47	chr1:152552175-152552225	MCF-7	breast:	n/a
48	chr1:152552175-152552225	AG09319	gingival:	n/a
49	chr1:152553096-152553146	HAEpiC	amniotic membrane:	n/a
50	chr1:152553096-152553146	IMR90	lung:	fetal

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

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

No data

Variant related genes	Relation type
LCE3C	TF binding region
LCE3E	TF binding region
LCE3B	TF binding region
LCE3D	TF binding region
LCE3C	CpG island
LCE3E	CpG island
LCE3B	CpG island
LCE3D	CpG island
ENSG00000187238	chromatin interactions

Extended variants
information (count: 633 )
Associated
traits (count: 121 )

Variant overlapped rSNPs/rCNVs (count:633 , 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	rs375043777	chr1:152540310-152540311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs111811835	chr1:152540319-152540320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs562977490	chr1:152540433-152540434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs531440003	chr1:152540455-152540456	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs200629152	chr1:152540462-152540463	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs7416330	chr1:152540522-152540523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs564902217	chr1:152540585-152540586	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs527584580	chr1:152540604-152540605	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs73005808	chr1:152540615-152540616	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs566964235	chr1:152540641-152540642	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs529638713	chr1:152540792-152540793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs549641238	chr1:152540833-152540834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs531874366	chr1:152540910-152540911	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs569720397	chr1:152540925-152540926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs189773913	chr1:152540933-152540934	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs141396386	chr1:152540938-152540939	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs150245640	chr1:152540971-152540972	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs375566367	chr1:152541022-152541023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs75257417	chr1:152541054-152541055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs72700982	chr1:152541062-152541063	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs183090908	chr1:152541068-152541069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs543027361	chr1:152541074-152541075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs561841770	chr1:152541087-152541088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs145791637	chr1:152541094-152541095	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs576501540	chr1:152541160-152541161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs545124938	chr1:152541165-152541166	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs545323616	chr1:152541226-152541227	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs148965535	chr1:152541279-152541280	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs187765014	chr1:152541291-152541292	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs540974983	chr1:152541318-152541319	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs192074418	chr1:152541375-152541376	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs547433669	chr1:152541504-152541505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs59063562	chr1:152541515-152541516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs569523941	chr1:152541561-152541562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs10465795	chr1:152541574-152541575	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs187907519	chr1:152541620-152541621	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs143708131	chr1:152541623-152541624	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs534366385	chr1:152541657-152541658	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs148096090	chr1:152541664-152541665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs192963895	chr1:152541675-152541676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs536515701	chr1:152541679-152541680	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs184849723	chr1:152541683-152541684	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs74577193	chr1:152541704-152541705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs77755198	chr1:152541705-152541706	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs79309557	chr1:152541706-152541707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs576318212	chr1:152541743-152541744	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs545526201	chr1:152541744-152541745	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs188137282	chr1:152541745-152541746	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs4357532	chr1:152541803-152541804	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs540813847	chr1:152541875-152541876	Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:121)

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
Non-syndromic sensorineural hearing loss	18451855	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152539400-152541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:152541800-152542400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:152542000-152544400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
4	chr1:152542400-152543000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:152543000-152552600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:152546400-152547000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:152547000-152552400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:152549400-152549800	Enhancers	GM12878-XiMat	blood
9	chr1:152549400-152550800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:152549400-152551400	Enhancers	HSMMtube	muscle
11	chr1:152549400-152551600	Enhancers	HSMM	muscle
12	chr1:152549800-152551400	Weak transcription	GM12878-XiMat	blood
13	chr1:152550800-152555200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:152551400-152552600	Enhancers	GM12878-XiMat	blood
15	chr1:152551600-152552800	Weak transcription	HSMM	muscle
16	chr1:152552400-152553200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:152552400-152553400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:152552600-152553200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:152552600-152553200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:152552600-152553400	Enhancers	HMEC	breast
21	chr1:152552800-152553200	Enhancers	HSMM	muscle
22	chr1:152552800-152553400	Enhancers	NHEK	skin
23	chr1:152553400-152555000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:152553400-152555000	Weak transcription	HMEC	breast
25	chr1:152553400-152555200	Weak transcription	NHEK	skin
26	chr1:152555000-152555600	Flanking Active TSS	A549	lung
27	chr1:152555000-152555600	Enhancers	HMEC	breast
28	chr1:152555000-152555800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:152555200-152555600	Enhancers	NHEK	skin
30	chr1:152555400-152555600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:152555400-152555800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:152569600-152570200	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links