Variant report

Variant	esv3355423
Chromosome Location	chr1:153401528-153405726
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	ARID3A	chr1:153405377-153406198	K562	blood:	n/a	n/a
2	ATF1	chr1:153405647-153406276	K562	blood:	n/a	n/a
3	BHLHE40	chr1:153403613-153403905	K562	blood:	n/a	n/a
4	BHLHE40	chr1:153405547-153406281	K562	blood:	n/a	n/a
5	CBX3	chr1:153405394-153406110	K562	blood:	n/a	n/a
6	CCNT2	chr1:153405498-153406228	K562	blood:	n/a	n/a
7	CEBPD	chr1:153405458-153406339	K562	blood:	n/a	n/a
8	CEBPD	chr1:153405561-153406296	K562	blood:	n/a	n/a
9	CTCF	chr1:153403727-153403751	GM12891	blood:	n/a	n/a
10	CTCF	chr1:153401426-153401546	MCF-7	breast:	n/a	chr1:153401483-153401496
11	CTCF	chr1:153401419-153401548	K562	blood:	n/a	chr1:153401483-153401496
12	CTCF	chr1:153401427-153401530	MCF-7	breast:	n/a	chr1:153401483-153401496
13	CTCF	chr1:153401380-153401530	GM12872	blood:	n/a	chr1:153401483-153401496
14	CTCF	chr1:153401438-153401553	HepG2	liver:	n/a	chr1:153401483-153401496
15	CTCF	chr1:153401480-153401630	NHDF-neo	bronchial:	n/a	chr1:153401483-153401496
16	CTCF	chr1:153403688-153403774	GM19239	blood:	n/a	n/a
17	CTCF	chr1:153401380-153401530	AG04450	lung:	n/a	chr1:153401483-153401496
18	CTCF	chr1:153401400-153401550	GM12873	blood:	n/a	chr1:153401483-153401496
19	CTCF	chr1:153401310-153401684	H1-hESC	embryonic stem cell:	n/a	chr1:153401483-153401496
20	CTCF	chr1:153401400-153401550	WERI-Rb-1	eye:	n/a	chr1:153401483-153401496
21	CTCF	chr1:153401380-153401530	HRE	kidney:	n/a	chr1:153401483-153401496
22	CTCF	chr1:153401420-153401570	GM12873	blood:	n/a	chr1:153401483-153401496
23	CTCF	chr1:153401380-153401530	HEK293	kidney:	n/a	chr1:153401483-153401496
24	CTCF	chr1:153401460-153401610	HMF	breast:	n/a	chr1:153401483-153401496
25	CTCF	chr1:153401420-153401570	BE2_C	brain:	n/a	chr1:153401483-153401496
26	CTCF	chr1:153401400-153401550	BE2_C	brain:	n/a	chr1:153401483-153401496
27	CTCF	chr1:153401420-153401570	WERI-Rb-1	eye:	n/a	chr1:153401483-153401496
28	CTCF	chr1:153401440-153401590	SK-N-SH_RA	brain:	n/a	chr1:153401483-153401496
29	CTCF	chr1:153401380-153401530	HRPEpiC	eye:	n/a	chr1:153401483-153401496
30	CTCF	chr1:153401411-153401551	MCF-7	breast:	n/a	chr1:153401483-153401496
31	CTCF	chr1:153401500-153401650	NHEK	skin:	n/a	n/a
32	CTCF	chr1:153401420-153401570	GM12871	blood:	n/a	chr1:153401483-153401496
33	CTCF	chr1:153401380-153401530	HCT-116	colon:	n/a	chr1:153401483-153401496
34	CTCF	chr1:153401400-153401550	Hela-S3	cervix:	n/a	chr1:153401483-153401496
35	CTCF	chr1:153403753-153403774	MCF-7	breast:	n/a	n/a
36	CTCF	chr1:153401305-153401611	H1-hESC	embryonic stem cell:	n/a	chr1:153401483-153401496
37	CTCF	chr1:153401380-153401530	HPAF	blood vessel:	n/a	chr1:153401483-153401496
38	CTCF	chr1:153403560-153403710	WERI-Rb-1	eye:	n/a	n/a
39	CTCF	chr1:153401580-153401730	HCM	heart:	n/a	n/a
40	CTCF	chr1:153401600-153401750	A549	lung:	n/a	n/a
41	CTCF	chr1:153402120-153402270	HEEpiC	esophagus:	n/a	n/a
42	CTCF	chr1:153401380-153401530	Caco-2	colon:	n/a	chr1:153401483-153401496
43	CTCF	chr1:153401439-153401539	MCF-7	breast:	n/a	chr1:153401483-153401496
44	CTCF	chr1:153403605-153403619	GM19239	blood:	n/a	n/a
45	CTCF	chr1:153401460-153401610	HepG2	liver:	n/a	chr1:153401483-153401496
46	CTCF	chr1:153401430-153401561	Hela-S3	cervix:	n/a	chr1:153401483-153401496
47	CTCF	chr1:153401440-153401590	HMEC	breast:	n/a	chr1:153401483-153401496
48	CTCF	chr1:153401380-153401686	K562	blood:	n/a	chr1:153401483-153401496
49	CTCF	chr1:153401600-153401750	BE2_C	brain:	n/a	n/a
50	CTCF	chr1:153401388-153401596	H1-hESC	embryonic stem cell:	n/a	chr1:153401483-153401496

No.	Distal block	Cell Line	Cell type
1	chr1:153333614..153335314-chr1:153401856..153404570,2	MCF-7	breast:
2	chr1:153404704..153408499-chr1:153408737..153412962,4	K562	blood:
3	chr1:153401556..153403433-chr1:153405617..153407706,2	K562	blood:
4	chr1:153335876..153338098-chr1:153401901..153404705,2	MCF-7	breast:
5	chr1:153333002..153335698-chr1:153404883..153407063,2	MCF-7	breast:
6	chr1:153401442..153403093-chr1:153408398..153410070,2	MCF-7	breast:
7	chr1:153402848..153404645-chr1:153405080..153406621,2	MCF-7	breast:
8	chr1:153365407..153367710-chr1:153401211..153403404,2	MCF-7	breast:
9	chr1:153401556..153403433-chr1:153405617..153407706,2	K562	blood:
10	chr1:153397872..153400976-chr1:153401654..153403402,3	MCF-7	breast:
11	chr1:153402848..153404645-chr1:153405080..153406621,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203781	TF binding region
ENSG00000203781	chromatin interactions
ENSG00000197364	chromatin interactions

Extended variants
information (count: 213 )
Associated
traits (count: 115 )

Variant overlapped rSNPs/rCNVs (count:213 , 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	rs540174256	chr1:153401531-153401532	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs36026521	chr1:153401535-153401536	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs553623715	chr1:153401540-153401541	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs567004530	chr1:153401565-153401566	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs112538681	chr1:153401572-153401573	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs3014824	chr1:153401588-153401589	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs555598522	chr1:153401610-153401611	Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs3006423	chr1:153401664-153401665	Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs370693008	chr1:153401666-153401667	Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs553491376	chr1:153401706-153401707	Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs576613101	chr1:153401707-153401708	Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs146671078	chr1:153401715-153401716	Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs149812724	chr1:153401774-153401775	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs184317455	chr1:153401798-153401799	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs557763838	chr1:153401826-153401827	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs113945641	chr1:153401843-153401844	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs540209532	chr1:153401935-153401936	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs145811830	chr1:153401948-153401949	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs573815418	chr1:153401971-153401972	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs201142481	chr1:153401994-153401995	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs141795199	chr1:153402015-153402016	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs562518293	chr1:153402039-153402040	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs192924619	chr1:153402055-153402056	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs551489422	chr1:153402059-153402060	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs184696791	chr1:153402060-153402061	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs533666419	chr1:153402065-153402066	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs539277341	chr1:153402113-153402114	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs570413776	chr1:153402155-153402156	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs147110499	chr1:153402188-153402189	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs549820204	chr1:153402209-153402210	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs567831655	chr1:153402257-153402258	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs535232137	chr1:153402317-153402318	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs553552691	chr1:153402323-153402324	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs138574170	chr1:153402340-153402341	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs539708691	chr1:153402345-153402346	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs189672938	chr1:153402412-153402413	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs73020416	chr1:153402463-153402464	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs562126207	chr1:153402500-153402501	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs375104297	chr1:153402513-153402514	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs556003816	chr1:153402526-153402527	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs180750937	chr1:153402586-153402587	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs541587945	chr1:153402610-153402611	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs78948762	chr1:153402619-153402620	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs533602218	chr1:153402671-153402672	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs552030608	chr1:153402672-153402673	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs576266781	chr1:153402673-153402674	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs150574056	chr1:153402686-153402687	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs563850462	chr1:153402751-153402752	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs531302986	chr1:153402752-153402753	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs143037309	chr1:153402768-153402769	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:115)

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
Ewing''s sarcoma	21437220	CNVD
Liposarcoma	21253554	CNVD
Non-small cell lung cancer	21385341	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
Non-syndromic sensorineural hearing loss	15273396	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
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
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
Chronic lymphocytic leukemia	22228453	CNVD
Glioblastoma multiforme	21138945	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	21611746	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelofibrosis	22110671	CNVD
Follicular lymphoma	20505157	CNVD
Liver carcinoma	19366792	CNVD
Neuroblastoma	18923191	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153401400-153403400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:153401600-153402200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:153401800-153402800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:153401800-153403000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:153402000-153402600	Enhancers	NHEK	skin
6	chr1:153402000-153403800	Enhancers	Esophagus	oesophagus
7	chr1:153402200-153403000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:153402600-153403600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:153403200-153407200	Enhancers	K562	blood
10	chr1:153403400-153403600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:153403400-153404000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:153403600-153403800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:153403600-153404000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:153404000-153404600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:153404000-153413800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:153404600-153406000	Enhancers	Placenta	Placenta
17	chr1:153405200-153406800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links