Variant report

Variant	nsv548524
Chromosome Location	chr1:189630723-189675416
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	chr1:189655218-189655237	K562	blood:	n/a	n/a
2	ATF1	chr1:189645110-189645131	K562	blood:	n/a	n/a
3	BACH1	chr1:189660033-189660067	K562	blood:	n/a	n/a
4	BCL3	chr1:189650561-189651101	A549	lung:	n/a	n/a
5	BRCA1	chr1:189640354-189640407	H1-hESC	embryonic stem cell:	n/a	n/a
6	CBX3	chr1:189631264-189631803	HCT-116	colon:	n/a	n/a
7	CBX3	chr1:189631288-189631734	HCT-116	colon:	n/a	n/a
8	CEBPB	chr1:189675215-189675438	HepG2	liver:	n/a	chr1:189675255-189675266
9	CEBPB	chr1:189650548-189650953	A549	lung:	n/a	n/a
10	CEBPB	chr1:189646472-189646806	HepG2	liver:	n/a	n/a
11	CEBPB	chr1:189631180-189631818	HCT-116	colon:	n/a	n/a
12	CEBPB	chr1:189675218-189675345	A549	lung:	n/a	chr1:189675255-189675266
13	CEBPB	chr1:189672613-189673256	IMR90	lung:	n/a	n/a
14	CEBPB	chr1:189651781-189651981	A549	lung:	n/a	n/a
15	CEBPB	chr1:189631210-189631769	HCT-116	colon:	n/a	n/a
16	CEBPB	chr1:189635284-189635346	HepG2	liver:	n/a	n/a
17	CTCF	chr1:189648040-189648190	HMF	breast:	n/a	n/a
18	CTCF	chr1:189647960-189648110	GM12875	blood:	n/a	n/a
19	CTCF	chr1:189658717-189658859	MCF-7	breast:	n/a	n/a
20	CTCF	chr1:189648000-189648150	GM12871	blood:	n/a	n/a
21	CTCF	chr1:189648057-189648171	GM13977	blood:	n/a	n/a
22	CTCF	chr1:189662384-189662565	MCF-7	breast:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
23	CTCF	chr1:189642480-189642630	MCF-7	breast:	n/a	n/a
24	CTCF	chr1:189642460-189642610	SAEC	small airway:	n/a	n/a
25	CTCF	chr1:189647960-189648110	GM12867	blood:	n/a	n/a
26	CTCF	chr1:189662340-189662490	Hela-S3	cervix:	n/a	chr1:189662475-189662488
27	CTCF	chr1:189648037-189648168	SK-N-SH_RA	brain:	n/a	n/a
28	CTCF	chr1:189648060-189648210	BE2_C	brain:	n/a	n/a
29	CTCF	chr1:189648049-189648195	GM12878	blood:	n/a	n/a
30	CTCF	chr1:189662380-189662530	RPTEC	kidney:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
31	CTCF	chr1:189631500-189631650	SAEC	small airway:	n/a	n/a
32	CTCF	chr1:189648091-189648145	Pancreas_OC	pancreas:	n/a	n/a
33	CTCF	chr1:189648040-189648190	SAEC	small airway:	n/a	n/a
34	CTCF	chr1:189648007-189648188	HepG2	liver:	n/a	n/a
35	CTCF	chr1:189648040-189648190	AG04449	skin:	n/a	n/a
36	CTCF	chr1:189648060-189648210	MCF-7	breast:	n/a	n/a
37	CTCF	chr1:189648140-189648290	A549	lung:	n/a	n/a
38	CTCF	chr1:189662360-189662510	BE2_C	brain:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
39	CTCF	chr1:189662420-189662570	HEEpiC	esophagus:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
40	CTCF	chr1:189648120-189648270	GM06990	blood:	n/a	n/a
41	CTCF	chr1:189642500-189642650	HCPEpiC	choroid plexus:	n/a	n/a
42	CTCF	chr1:189648020-189648170	HCPEpiC	choroid plexus:	n/a	n/a
43	CTCF	chr1:189642437-189642650	T-47D	breast:	n/a	n/a
44	CTCF	chr1:189648060-189648210	HVMF	connective:	n/a	n/a
45	CTCF	chr1:189662392-189662608	Gliobla	brain:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
46	CTCF	chr1:189648040-189648190	HRPEpiC	eye:	n/a	n/a
47	CTCF	chr1:189647800-189647950	NHEK	skin:	n/a	n/a
48	CTCF	chr1:189662279-189662762	MCF-7	breast:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
49	CTCF	chr1:189662481-189662525	HUVEC	blood vessel:	n/a	n/a
50	CTCF	chr1:189662440-189662590	HPF	lung:	n/a	chr1:189662475-189662488 chr1:189662473-189662491

No.	Distal block	Cell Line	Cell type
1	chr1:189630297..189631878-chr1:189633078..189635794,2	K562	blood:
2	chr1:189672702..189674835-chr1:189679900..189682761,2	MCF-7	breast:
3	chr1:189398440..189399083-chr1:189642226..189643036,4	MCF-7	breast:
4	chr1:189627826..189630498-chr1:189636599..189639267,2	MCF-7	breast:
5	chr1:189646033..189647879-chr5:175874488..175876371,2	MCF-7	breast:
6	chr1:189398509..189399144-chr1:189660311..189661261,2	MCF-7	breast:
7	chr1:189627801..189630516-chr1:189640573..189642596,2	MCF-7	breast:
8	chr1:189398408..189399387-chr1:189661985..189662829,2	MCF-7	breast:
9	chr1:189624367..189627091-chr1:189650312..189652304,2	MCF-7	breast:
10	chr1:189589226..189590045-chr1:189662088..189662866,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP73	TF binding region
ENSG00000113194	chromatin interactions
ENSG00000252553	chromatin interactions

Extended variants
information (count: 619 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:619 , 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	rs480025	chr1:189630723-189630724	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs563162761	chr1:189630740-189630741	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs531640147	chr1:189630749-189630750	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs571108170	chr1:189630768-189630769	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs538102952	chr1:189630796-189630797	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs548586479	chr1:189630835-189630836	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs579032	chr1:189630852-189630853	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs142422195	chr1:189630927-189630928	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs200891319	chr1:189630956-189630957	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs557000	chr1:189630967-189630968	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs536549141	chr1:189630989-189630990	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs538430742	chr1:189631062-189631063	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs542830624	chr1:189631085-189631086	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs186840242	chr1:189631125-189631126	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs575186237	chr1:189631172-189631173	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs537712378	chr1:189631179-189631180	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs374632150	chr1:189631207-189631208	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs191677096	chr1:189631265-189631266	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs184885354	chr1:189631315-189631316	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs189818958	chr1:189631333-189631334	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs536901109	chr1:189631343-189631344	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs577549232	chr1:189631348-189631349	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs546400936	chr1:189631361-189631362	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs563044193	chr1:189631368-189631369	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs532047653	chr1:189631380-189631381	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs368428445	chr1:189631400-189631401	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs548559993	chr1:189631414-189631415	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs79165133	chr1:189631433-189631434	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs193194561	chr1:189631461-189631462	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs185542333	chr1:189631494-189631495	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs547518930	chr1:189631497-189631498	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs189429963	chr1:189631501-189631502	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs695185	chr1:189631567-189631568	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs115434139	chr1:189631582-189631583	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs146840616	chr1:189631629-189631630	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs693683	chr1:189631634-189631635	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs541458277	chr1:189631670-189631671	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs554563548	chr1:189631701-189631702	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs574415816	chr1:189631705-189631706	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs533541533	chr1:189631707-189631708	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs553940205	chr1:189631713-189631714	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs560173566	chr1:189631778-189631779	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs180779831	chr1:189631784-189631785	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs545880675	chr1:189631812-189631813	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs184948560	chr1:189631816-189631817	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs140645712	chr1:189631833-189631834	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs542557845	chr1:189631840-189631841	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs188246390	chr1:189631901-189631902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs527712585	chr1:189631946-189631947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs144517915	chr1:189631973-189631974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	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
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
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
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	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
Hepatocellular carcinoma	18803288	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
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Metanephric adenoma	20802469	CNVD
Melanoma	20688739	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21611746	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	17899364	CNVD
Non-small cell lung cancer	19010865	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Lung adenocarcinoma	17086460	CNVD
Glioblastoma multiforme	22286061	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189629400-189641400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:189636400-189636600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:189639200-189639400	Enhancers	A549	lung
4	chr1:189640400-189640600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:189640800-189641000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:189645000-189645400	Enhancers	Fetal Heart	heart
7	chr1:189649600-189650400	Enhancers	A549	lung
8	chr1:189650200-189651200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:189650400-189650600	Flanking Active TSS	A549	lung
10	chr1:189650400-189651000	Enhancers	HepG2	liver
11	chr1:189650600-189651000	Active TSS	A549	lung
12	chr1:189651200-189651600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:189651600-189652000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:189665400-189666400	Active TSS	Placenta	Placenta
15	chr1:189666400-189666600	Flanking Active TSS	Placenta	Placenta
16	chr1:189675200-189676200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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