Variant report

Variant	esv3486919
Chromosome Location	chr12:48725070-48728735
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:122)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr12:48728652-48728898	GM12878	blood:	n/a	n/a
2	CEBPB	chr12:48728691-48728961	K562	blood:	n/a	chr12:48728871-48728882
3	CEBPB	chr12:48728714-48729014	K562	blood:	n/a	chr12:48728871-48728882
4	EBF1	chr12:48725328-48725412	GM12878	blood:	n/a	n/a
5	EBF1	chr12:48728682-48729079	GM12878	blood:	n/a	chr12:48728882-48728893
6	IRF3	chr12:48724983-48725087	GM12878	blood:	n/a	n/a
7	NR2F2	chr12:48725487-48725856	K562	blood:	n/a	n/a
8	NR2F2	chr12:48725531-48725788	K562	blood:	n/a	n/a
9	PBX3	chr12:48728644-48728820	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:48724588-48725119	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr12:48728662-48728856	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:48728722-48728977	K562	blood:	n/a	n/a
13	POLR2A	chr12:48727353-48727474	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:48728447-48730748	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:48728648-48728848	MCF10A-Er-Src	breast:	n/a	n/a
16	ZNF143	chr12:48728693-48728945	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48727676-48727726	PFSK-1	brain:	n/a
2	chr12:48727676-48727726	HCF	heart:	n/a
3	chr12:48725269-48725319	AG09319	gingival:	n/a
4	chr12:48725269-48725319	AG04450	lung:	fetal
5	chr12:48725269-48725319	HCF	heart:	n/a
6	chr12:48727676-48727726	HRCEpiC	kidney:	n/a
7	chr12:48725269-48725319	PANC-1	pancreas:	n/a
8	chr12:48727676-48727726	AG09309	skin:	n/a
9	chr12:48727676-48727726	AG09319	gingival:	n/a
10	chr12:48725269-48725319	HEK293	kidney:	embryo
11	chr12:48727676-48727726	LNCaP	prostate:	n/a
12	chr12:48725269-48725319	GM12891	blood:	n/a
13	chr12:48727676-48727726	SKMC	muscle:	n/a
14	chr12:48727676-48727726	ECC-1	luminal epithelium:	n/a
15	chr12:48725269-48725319	SAEC	small airway:	n/a
16	chr12:48725269-48725319	GM06990	blood:	n/a
17	chr12:48727676-48727726	HCM	heart:	n/a
18	chr12:48725269-48725319	HEEpiC	esophagus:	n/a
19	chr12:48727676-48727726	AG04449	skin:	fetal
20	chr12:48727676-48727726	HL-60	blood:	n/a
21	chr12:48727676-48727726	HepG2	liver:	n/a
22	chr12:48725269-48725319	LNCaP	prostate:	n/a
23	chr12:48725269-48725319	MCF10A-Er-Src	breast:	n/a
24	chr12:48727676-48727726	HRPEpiC	eye:	n/a
25	chr12:48727676-48727726	T-47D	breast:	n/a
26	chr12:48727676-48727726	U87	brain:	n/a
27	chr12:48727676-48727726	MCF10A-Er-Src	breast:	n/a
28	chr12:48727676-48727726	NT2-D1	testis:	n/a
29	chr12:48727676-48727726	CMK	blood:	n/a
30	chr12:48727676-48727726	GM19239	blood:	n/a
31	chr12:48727676-48727726	NHBE	bronchial:	n/a
32	chr12:48727676-48727726	NB4	blood:	n/a
33	chr12:48727676-48727726	GM06990	blood:	n/a
34	chr12:48727676-48727726	HEEpiC	esophagus:	n/a
35	chr12:48727676-48727726	SAEC	small airway:	n/a
36	chr12:48725269-48725319	GM12878	blood:	n/a
37	chr12:48725269-48725319	SKMC	muscle:	n/a
38	chr12:48725269-48725319	NH-A	brain:	n/a
39	chr12:48727676-48727726	ovcar-3	ovarian:	n/a
40	chr12:48725269-48725319	HRPEpiC	eye:	n/a
41	chr12:48727676-48727726	HMEC	breast:	n/a
42	chr12:48725269-48725319	HMEC	breast:	n/a
43	chr12:48727676-48727726	Hela-S3	cervix:	n/a
44	chr12:48727676-48727726	PrEC	prostate:	n/a
45	chr12:48727676-48727726	SK-N-MC	brain:	n/a
46	chr12:48725269-48725319	NHBE	bronchial:	n/a
47	chr12:48725269-48725319	HNPCEpiC	eye:	n/a
48	chr12:48727676-48727726	SK-N-SH	brain:	n/a
49	chr12:48725269-48725319	HPAEpiC	pulmonary alveolar:	n/a
50	chr12:48727676-48727726	K562	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48723401..48726015-chr12:48731031..48733987,2	K562	blood:
2	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:
3	chr12:48723517..48726373-chr12:48743462..48746154,2	MCF-7	breast:
4	chr12:48595137..48597304-chr12:48723184..48725728,2	K562	blood:
5	chr12:48724931..48726830-chr12:48727144..48729344,2	MCF-7	breast:
6	chr12:48724124..48726924-chr12:48729668..48731393,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258273	TF binding region
ENSG00000258273	CpG island
ENSG00000257735	chromatin interactions
ENSG00000172640	chromatin interactions
ENSG00000167528	chromatin interactions
ENSG00000258273	chromatin interactions

Extended variants
information (count: 86 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:86 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534666252	chr12:48725070-48725071	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs564256082	chr12:48725084-48725085	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs146977795	chr12:48725111-48725112	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs372649859	chr12:48725146-48725147	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs79264801	chr12:48725154-48725155	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs538008585	chr12:48725191-48725192	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs574131978	chr12:48725263-48725264	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs542648913	chr12:48725313-48725314	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs142704044	chr12:48725314-48725315	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs553292561	chr12:48725315-48725316	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs367563481	chr12:48725352-48725353	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs573262196	chr12:48725378-48725379	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs545457223	chr12:48725405-48725406	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs563957273	chr12:48725418-48725419	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs555444928	chr12:48725479-48725480	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs370624293	chr12:48725480-48725481	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs112939020	chr12:48725482-48725483	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs144425258	chr12:48725488-48725489	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs111449445	chr12:48725490-48725491	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs71080104	chr12:48725491-48725492	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs71445743	chr12:48725630-48725631	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs376820368	chr12:48725702-48725703	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs543340350	chr12:48725723-48725724	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs375826568	chr12:48725740-48725741	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs540505018	chr12:48725751-48725752	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs529146064	chr12:48725759-48725760	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs561838171	chr12:48725765-48725766	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs375366755	chr12:48726104-48726105	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs561450977	chr12:48726123-48726124	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs111286049	chr12:48726125-48726126	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs112335222	chr12:48726232-48726233	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs371930661	chr12:48726502-48726503	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs201265187	chr12:48726519-48726520	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs565641975	chr12:48726610-48726611	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs528188311	chr12:48726613-48726614	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs112872232	chr12:48726649-48726650	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs113781161	chr12:48726657-48726658	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs200695345	chr12:48726776-48726777	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs376813822	chr12:48727103-48727104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs558424110	chr12:48727189-48727190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs12231094	chr12:48727246-48727247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs61942768	chr12:48727424-48727425	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs551483649	chr12:48727440-48727441	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs571895605	chr12:48727560-48727561	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs537635571	chr12:48727561-48727562	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs564480963	chr12:48727599-48727600	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs373747312	chr12:48727600-48727601	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs543391157	chr12:48727607-48727608	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs71445746	chr12:48727609-48727610	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs567973137	chr12:48727623-48727624	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	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
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	16616336	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48723800-48736600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48724200-48734400	Weak transcription	Thymus	Thymus
3	chr12:48724400-48736000	Weak transcription	Fetal Stomach	stomach
4	chr12:48724600-48725200	Enhancers	Hela-S3	cervix
5	chr12:48725000-48725200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr12:48725000-48725200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:48725200-48734600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:48725200-48735800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:48725200-48736800	Weak transcription	Hela-S3	cervix
10	chr12:48728000-48736000	Weak transcription	HSMMtube	muscle
11	chr12:48728400-48728600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr12:48728400-48728600	Weak transcription	Right Ventricle	heart
13	chr12:48728400-48728800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr12:48728400-48729000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:48728400-48729200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:48728400-48729200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:48728400-48731200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:48728600-48728800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:48728600-48728800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr12:48728600-48728800	Enhancers	Right Ventricle	heart
21	chr12:48728600-48728800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr12:48728600-48729000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr12:48728600-48729000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:48728600-48729000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:48728600-48729000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr12:48728600-48729000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:48728600-48729000	Enhancers	Spleen	Spleen
28	chr12:48728600-48734000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:48728600-48734800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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