Variant report

Variant	nsv527632
Chromosome Location	chr12:690473-698634
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	chr12:694354-694408	HepG2	liver:	n/a	n/a
2	ARID3A	chr12:694614-695166	HepG2	liver:	n/a	n/a
3	ARID3A	chr12:697080-697280	K562	blood:	n/a	n/a
4	BHLHE40	chr12:694620-695033	HepG2	liver:	n/a	n/a
5	BHLHE40	chr12:696922-697215	K562	blood:	n/a	n/a
6	BHLHE40	chr12:692462-692966	HepG2	liver:	n/a	n/a
7	CBX3	chr12:696874-697407	K562	blood:	n/a	n/a
8	CBX3	chr12:697859-698175	K562	blood:	n/a	n/a
9	CCNT2	chr12:696936-697321	K562	blood:	n/a	n/a
10	CEBPB	chr12:694642-695009	HepG2	liver:	n/a	chr12:694869-694877
11	CEBPB	chr12:694703-694927	HepG2	liver:	n/a	chr12:694869-694877
12	CEBPD	chr12:694704-695000	HepG2	liver:	n/a	n/a
13	CEBPD	chr12:692506-692775	HepG2	liver:	n/a	n/a
14	CHD2	chr12:694717-695016	HepG2	liver:	n/a	n/a
15	CTCF	chr12:693954-694007	GM20000	blood:	n/a	n/a
16	CTCF	chr12:694322-694390	Lung_OC	lung:	n/a	n/a
17	CTCF	chr12:692379-692380	GM19239	blood:	n/a	n/a
18	CTCF	chr12:692385-692392	GM19239	blood:	n/a	n/a
19	CTCF	chr12:694885-695112	HepG2	liver:	n/a	n/a
20	CTCF	chr12:694023-694038	GM20000	blood:	n/a	n/a
21	CTCF	chr12:690500-690650	GM12864	blood:	n/a	n/a
22	CTCF	chr12:691842-691889	LNCaP	prostate:	n/a	n/a
23	CTCF	chr12:694952-695027	HepG2	liver:	n/a	n/a
24	CTCF	chr12:690420-690570	GM12868	blood:	n/a	n/a
25	CTCF	chr12:692407-692426	GM19239	blood:	n/a	n/a
26	CUX1	chr12:697079-697086	K562	blood:	n/a	n/a
27	E2F6	chr12:692570-692701	K562	blood:	n/a	n/a
28	EBF1	chr12:698508-698865	GM12878	blood:	n/a	chr12:698683-698694
29	EGR1	chr12:695648-695814	K562	blood:	n/a	chr12:695726-695740 chr12:695728-695738 chr12:695722-695744 chr12:695727-695740 chr12:695726-695741 chr12:695727-695740 chr12:695728-695739
30	EGR1	chr12:695628-695853	K562	blood:	n/a	chr12:695726-695740 chr12:695728-695738 chr12:695722-695744 chr12:695727-695740 chr12:695726-695741 chr12:695727-695740 chr12:695728-695739
31	EP300	chr12:694624-695146	HepG2	liver:	n/a	chr12:694857-694867
32	EP300	chr12:692316-692935	HepG2	liver:	n/a	n/a
33	EP300	chr12:692471-692873	HepG2	liver:	n/a	n/a
34	EP300	chr12:694568-695205	HepG2	liver:	n/a	chr12:694857-694867
35	EP300	chr12:694562-695186	HepG2	liver:	n/a	chr12:694857-694867
36	EP300	chr12:692474-692856	HepG2	liver:	n/a	n/a
37	EP300	chr12:696932-697312	K562	blood:	n/a	chr12:697232-697242
38	EP300	chr12:694524-695153	A549	lung:	n/a	chr12:694857-694867
39	FOSL2	chr12:694441-695143	HepG2	liver:	n/a	chr12:694784-694795 chr12:694870-694879
40	FOSL2	chr12:692119-692907	HepG2	liver:	n/a	n/a
41	FOSL2	chr12:691320-691904	HepG2	liver:	n/a	n/a
42	FOSL2	chr12:691294-692907	HepG2	liver:	n/a	n/a
43	FOSL2	chr12:694507-695096	HepG2	liver:	n/a	chr12:694784-694795 chr12:694870-694879
44	FOXA1	chr12:694562-695174	HepG2	liver:	n/a	n/a
45	FOXA1	chr12:694492-695135	HepG2	liver:	n/a	n/a
46	FOXA1	chr12:692421-692815	HepG2	liver:	n/a	n/a
47	FOXA1	chr12:694525-695159	HepG2	liver:	n/a	n/a
48	FOXA1	chr12:694534-695193	HepG2	liver:	n/a	n/a
49	FOXA1	chr12:692384-692903	HepG2	liver:	n/a	n/a
50	FOXA2	chr12:694370-695190	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:561825..562818-chr12:694443..695023,2	MCF-7	breast:
2	chr12:686739..689998-chr12:691265..694339,4	K562	blood:
3	chr12:696407..698451-chr12:743928..745643,2	MCF-7	breast:
4	chr12:691109..693273-chr12:695589..698254,2	K562	blood:
5	chr12:689801..692487-chr12:897629..900163,2	K562	blood:
6	chr12:688710..691360-chr12:698312..700613,2	K562	blood:
7	chr12:693107..696400-chr12:699400..702911,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM5A-3	chr12:695414-695652	ENSG00000256020.1
2	lnc-B4GALNT3-4	chr12:690328-690539	l_576_chr12:669260-707688_adipose
3	lnc-KDM5A-3	chr12:695031-695164	ENSG00000256020.1

Variant related genes	Relation type
ENSG00000256020	TF binding region
ENSG00000255825	TF binding region
ENSG00000255825	chromatin interactions
ENSG00000238370	chromatin interactions
ENSG00000256020	chromatin interactions

Extended variants
information (count: 388 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:388 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2535429	chr12:690473-690474	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs575358649	chr12:690484-690485	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs532709656	chr12:690485-690486	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs184703487	chr12:690519-690520	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs558031301	chr12:690545-690546	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs573153070	chr12:690560-690561	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs369452989	chr12:690579-690580	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs561691885	chr12:690587-690588	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs528883157	chr12:690655-690656	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs59288136	chr12:690677-690678	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs532909096	chr12:690689-690690	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs552328927	chr12:690690-690691	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs139732656	chr12:690700-690701	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs116534537	chr12:690703-690704	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs556054846	chr12:690729-690730	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs546909094	chr12:690795-690796	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs551290571	chr12:690799-690800	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs386759366	chr12:690820-690821	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs535493575	chr12:690821-690822	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs189328246	chr12:690879-690880	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs569252789	chr12:690911-690912	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs370923872	chr12:690913-690914	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs144448441	chr12:690914-690915	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs573090776	chr12:690946-690947	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs540484621	chr12:690947-690948	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs180824144	chr12:690987-690988	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs116385040	chr12:691029-691030	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs61919370	chr12:691072-691073	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs184792441	chr12:691103-691104	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs577299844	chr12:691113-691114	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs544716876	chr12:691131-691132	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs377499027	chr12:691143-691144	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs528666626	chr12:691153-691154	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs547233529	chr12:691165-691166	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs77036095	chr12:691177-691178	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs529641413	chr12:691184-691185	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs550677695	chr12:691273-691274	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs539842530	chr12:691274-691275	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs146118781	chr12:691305-691306	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs61919371	chr12:691320-691321	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs61919372	chr12:691339-691340	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs530644273	chr12:691363-691364	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs61919373	chr12:691419-691420	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs71447500	chr12:691440-691441	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs533964540	chr12:691458-691459	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs372460863	chr12:691459-691460	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs71435015	chr12:691497-691498	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs2535430	chr12:691498-691499	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs375042888	chr12:691499-691500	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs78748175	chr12:691520-691521	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Glaucoma	21310917	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Squamous cell cancer	19607727	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Mental retardation	17847001	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
abnormal development	18461090	CNVD
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
small cell lung cancer	20016488	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21509527	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Ovarian cancer	21720365	CNVD
Myelodysplastic syndrome	21251322	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pleomorphic liposarcoma	18784837	CNVD

Chromatin state (count:134 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:682000-690600	Enhancers	HepG2	liver
2	chr12:682000-692800	Weak transcription	Gastric	stomach
3	chr12:685800-692200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:685800-692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:685800-694400	Weak transcription	Spleen	Spleen
6	chr12:685800-700400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:686000-692200	Weak transcription	Pancreas	Pancrea
8	chr12:686000-692600	Weak transcription	Right Atrium	heart
9	chr12:686000-694400	Weak transcription	GM12878-XiMat	blood
10	chr12:686000-695400	Weak transcription	Esophagus	oesophagus
11	chr12:686200-690800	Weak transcription	Psoas Muscle	Psoas
12	chr12:686200-694800	Weak transcription	Stomach Mucosa	stomach
13	chr12:686200-716200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:686600-700400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:687600-691600	Enhancers	Fetal Heart	heart
16	chr12:688600-690600	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:688800-696800	Weak transcription	Brain Substantia Nigra	brain
18	chr12:688800-700400	Weak transcription	Brain Anterior Caudate	brain
19	chr12:689000-692400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:689000-699600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:689200-692400	Weak transcription	A549	lung
22	chr12:689200-700400	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:689600-692200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:689800-691200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr12:689800-691400	Enhancers	Left Ventricle	heart
26	chr12:689800-691600	Enhancers	Fetal Muscle Trunk	muscle
27	chr12:690000-691400	Enhancers	Right Ventricle	heart
28	chr12:690000-694400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:690000-696800	Enhancers	Liver	Liver
30	chr12:690400-691200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:690400-693800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:690400-694600	Weak transcription	K562	blood
33	chr12:690400-697800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:690600-690800	Flanking Active TSS	HepG2	liver
35	chr12:690600-691600	Enhancers	Fetal Muscle Leg	muscle
36	chr12:690800-691000	Enhancers	Psoas Muscle	Psoas
37	chr12:690800-691000	Enhancers	HepG2	liver
38	chr12:691000-691200	Flanking Active TSS	HepG2	liver
39	chr12:691000-693800	Weak transcription	Psoas Muscle	Psoas
40	chr12:691200-691600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr12:691200-692400	Enhancers	HepG2	liver
42	chr12:691400-692400	Weak transcription	Right Ventricle	heart
43	chr12:691400-692800	Weak transcription	Left Ventricle	heart
44	chr12:691600-692000	Weak transcription	Fetal Heart	heart
45	chr12:691600-692000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:691600-692000	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:691600-692200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:692000-692400	Enhancers	Fetal Muscle Trunk	muscle
49	chr12:692000-693200	Enhancers	Fetal Heart	heart
50	chr12:692000-693600	Enhancers	Fetal Muscle Leg	muscle

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