Variant report

Variant	esv3493509
Chromosome Location	chr12:58027949-58029355
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:58028220-58028370	AG10803	skin:	n/a	n/a
2	CTCF	chr12:58027980-58028130	SAEC	small airway:	n/a	n/a
3	CTCF	chr12:58028194-58028325	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr12:58028231-58028301	HepG2	liver:	n/a	n/a
5	CTCF	chr12:58028039-58028059	GM10266	blood:	n/a	n/a
6	CTCF	chr12:58028140-58028290	HCT-116	colon:	n/a	n/a
7	CTCF	chr12:58028198-58028352	HepG2	liver:	n/a	n/a
8	JUN	chr12:58028737-58028962	HepG2	liver:	n/a	chr12:58028877-58028890
9	JUND	chr12:58028727-58029014	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57940164..57942070-chr12:58025601..58028102,2	MCF-7	breast:
2	chr12:58026571..58028240-chr12:58118727..58121626,2	MCF-7	breast:
3	chr12:58026019..58028946-chr12:58148453..58151531,3	K562	blood:
4	chr12:57935626..57940631-chr12:58026197..58030320,5	K562	blood:
5	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:
6	chr12:57983391..57985108-chr12:58026747..58028430,2	MCF-7	breast:
7	chr12:58004618..58008024-chr12:58024930..58028098,5	MCF-7	breast:
8	chr12:58024113..58026472-chr12:58028228..58030289,2	K562	blood:
9	chr12:57983573..57987941-chr12:58024849..58028209,5	MCF-7	breast:
10	chr12:57908910..57916403-chr12:58022622..58028885,15	K562	blood:
11	chr12:57908910..57916122-chr12:58022622..58031573,17	K562	blood:

No data

Variant related genes	Relation type
B4GALNT1	TF binding region
ENSG00000139266	chromatin interactions
ENSG00000240771	chromatin interactions
ENSG00000135446	chromatin interactions
ENSG00000178498	chromatin interactions
ENSG00000166986	chromatin interactions
ENSG00000135454	chromatin interactions
ENSG00000175197	chromatin interactions
ENSG00000208028	chromatin interactions
ENSG00000257499	chromatin interactions
ENSG00000175203	chromatin interactions
ENSG00000255737	chromatin interactions
ENSG00000166987	chromatin interactions
ENSG00000166908	chromatin interactions

Extended variants
information (count: 52 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:52 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547092766	chr12:58027953-58027954	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
2	rs143198408	chr12:58027965-58027966	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
3	rs201486187	chr12:58027992-58027993	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
4	rs543450930	chr12:58028020-58028021	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
5	rs12296818	chr12:58028037-58028038	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs577088012	chr12:58028044-58028045	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
7	rs4397894	chr12:58028049-58028050	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
8	rs185185790	chr12:58028051-58028052	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
9	rs149575786	chr12:58028053-58028054	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
10	rs142710812	chr12:58028055-58028056	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
11	rs145038850	chr12:58028058-58028059	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
12	rs548364305	chr12:58028064-58028065	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
13	rs559664384	chr12:58028080-58028081	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
14	rs561052349	chr12:58028126-58028127	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
15	rs575572182	chr12:58028142-58028143	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
16	rs531654401	chr12:58028234-58028235	Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
17	rs544560489	chr12:58028268-58028269	Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
18	rs571279964	chr12:58028283-58028284	Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
19	rs372349757	chr12:58028304-58028305	Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
20	rs202216644	chr12:58028342-58028343	Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
21	rs34271193	chr12:58028361-58028362	Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs200259419	chr12:58028363-58028364	Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
23	rs189218233	chr12:58028380-58028381	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
24	rs536448766	chr12:58028452-58028453	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
25	rs555159115	chr12:58028463-58028464	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
26	rs192575585	chr12:58028466-58028467	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
27	rs537113899	chr12:58028487-58028488	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
28	rs147522030	chr12:58028494-58028495	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
29	rs369422168	chr12:58028513-58028514	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
30	rs576796581	chr12:58028535-58028536	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
31	rs140083336	chr12:58028556-58028557	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
32	rs372285811	chr12:58028592-58028593	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
33	rs184828989	chr12:58028596-58028597	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
34	rs188074810	chr12:58028743-58028744	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
35	rs12578587	chr12:58028746-58028747	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs181073477	chr12:58028770-58028771	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
37	rs563109625	chr12:58028825-58028826	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
38	rs531714155	chr12:58028852-58028853	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
39	rs6581147	chr12:58028863-58028864	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs528430725	chr12:58028867-58028868	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
41	rs114637968	chr12:58028914-58028915	Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
42	rs532447160	chr12:58028948-58028949	Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
43	rs547720602	chr12:58029058-58029059	Weak transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
44	rs566252797	chr12:58029065-58029066	Weak transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
45	rs201752146	chr12:58029104-58029105	Weak transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
46	rs12298852	chr12:58029243-58029244	Weak transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
47	rs12312189	chr12:58029250-58029251	Weak transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
48	rs7958927	chr12:58029261-58029262	Weak transcription	Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs377404253	chr12:58029277-58029278	Weak transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
50	rs548819596	chr12:58029283-58029284	Weak transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
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
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	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
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	18632612	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Bladder cancer	21909424	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Autism	20531469	CNVD
Rhabdomyosarcoma	16790082	CNVD
Renal cell carcinoma	18765545	CNVD
Urothelial cell carcinoma	18451213	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21138945	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Leukemia	18628472	CNVD
Glioblastoma multiforme	22291905	CNVD
Glioblastoma multiforme	19435819	CNVD
Myelofibrosis	22110671	CNVD
Phyllodes tumor	17334353	CNVD
Glaucoma	21310917	CNVD
Breast cancer	16272173	CNVD
Mental retardation	19951919	CNVD
Glaucoma	21447600	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Developmental delay	21267005	CNVD
12q14 microdeletion syndrome	21267005	CNVD
Developmental delay	19277063	CNVD
Dwarfism	19277063	CNVD
Fibroblasts	20926602	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Glycogen storage disease	18421352	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Glioblastoma multiforme	20080666	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	17133270	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58027200-58028000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:58027200-58033600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:58027600-58028200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:58027600-58034000	Weak transcription	K562	blood
5	chr12:58027800-58028000	Flanking Active TSS	Hela-S3	cervix
6	chr12:58027800-58030600	Weak transcription	A549	lung
7	chr12:58028000-58028200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood

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