Variant report

Variant	esv1826200
Chromosome Location	chr12:59916767-59946206
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:183)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr12:59928674-59929037	GM12878	blood:	n/a	n/a
2	BCL3	chr12:59928657-59928995	GM12878	blood:	n/a	n/a
3	BCL3	chr12:59928231-59928552	GM12878	blood:	n/a	n/a
4	BRCA1	chr12:59940309-59940328	GM12878	blood:	n/a	n/a
5	CEBPB	chr12:59928811-59928850	A549	lung:	n/a	n/a
6	CTCF	chr12:59923861-59923887	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F4	chr12:59920453-59920597	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA1	chr12:59942803-59943136	HepG2	liver:	n/a	n/a
9	FOXA1	chr12:59942809-59943016	T-47D	breast:	n/a	n/a
10	IRF1	chr12:59922062-59922098	K562	blood:	n/a	n/a
11	MAZ	chr12:59919589-59919635	HepG2	liver:	n/a	n/a
12	MYC	chr12:59923345-59923478	MCF10A-Er-Src	breast:	n/a	n/a
13	NFATC1	chr12:59943727-59944028	GM12878	blood:	n/a	n/a
14	PBX3	chr12:59943765-59943962	GM12878	blood:	n/a	n/a
15	PBX3	chr12:59930497-59930722	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:59944465-59944495	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:59920291-59920329	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr12:59918924-59919124	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr12:59944605-59944684	MCF10A-Er-Src	breast:	n/a	n/a
20	TCF3	chr12:59943733-59944009	GM12878	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:59925037-59925087	IMR90	lung:	fetal
2	chr12:59924853-59924903	SK-N-MC	brain:	n/a
3	chr12:59925037-59925087	AG09319	gingival:	n/a
4	chr12:59924853-59924903	BE2_C	brain:	n/a
5	chr12:59925323-59925373	PANC-1	pancreas:	n/a
6	chr12:59925037-59925087	AG04449	skin:	fetal
7	chr12:59924853-59924903	LNCaP	prostate:	n/a
8	chr12:59925037-59925087	NHBE	bronchial:	n/a
9	chr12:59925323-59925373	SK-N-SH_RA	brain:	n/a
10	chr12:59924853-59924903	K562	blood:	n/a
11	chr12:59925037-59925087	T-47D	breast:	n/a
12	chr12:59925323-59925373	ECC-1	luminal epithelium:	n/a
13	chr12:59925037-59925087	AG04450	lung:	fetal
14	chr12:59925037-59925087	U87	brain:	n/a
15	chr12:59925037-59925087	ECC-1	luminal epithelium:	n/a
16	chr12:59925037-59925087	GM12892	blood:	n/a
17	chr12:59925037-59925087	ProgFib	skin:	n/a
18	chr12:59925037-59925087	GM19239	blood:	n/a
19	chr12:59924853-59924903	HEEpiC	esophagus:	n/a
20	chr12:59925037-59925087	LNCaP	prostate:	n/a
21	chr12:59925037-59925087	NT2-D1	testis:	n/a
22	chr12:59924853-59924903	ProgFib	skin:	n/a
23	chr12:59924853-59924903	SK-N-SH	brain:	n/a
24	chr12:59924853-59924903	RPTEC	kidney:	n/a
25	chr12:59925037-59925087	HIPEpiC	eye:	n/a
26	chr12:59925323-59925373	K562	blood:	n/a
27	chr12:59925323-59925373	MCF10A-Er-Src	breast:	n/a
28	chr12:59925037-59925087	HL-60	blood:	n/a
29	chr12:59924853-59924903	Jurkat	blood:	n/a
30	chr12:59925323-59925373	HepG2	liver:	n/a
31	chr12:59924853-59924903	GM12878	blood:	n/a
32	chr12:59924853-59924903	T-47D	breast:	n/a
33	chr12:59924853-59924903	HCPEpiC	choroid plexus:	n/a
34	chr12:59924853-59924903	HEK293	kidney:	embryo
35	chr12:59924853-59924903	HIPEpiC	eye:	n/a
36	chr12:59925037-59925087	HMEC	breast:	n/a
37	chr12:59925323-59925373	SKMC	muscle:	n/a
38	chr12:59924853-59924903	A549	lung:	n/a
39	chr12:59925323-59925373	HEK293	kidney:	embryo
40	chr12:59924853-59924903	HUVEC	blood vessel:	n/a
41	chr12:59924853-59924903	Caco-2	colon:	n/a
42	chr12:59925037-59925087	HCF	heart:	n/a
43	chr12:59925037-59925087	GM06990	blood:	n/a
44	chr12:59924853-59924903	GM19239	blood:	n/a
45	chr12:59925037-59925087	Hela-S3	cervix:	n/a
46	chr12:59925037-59925087	SK-N-SH_RA	brain:	n/a
47	chr12:59925037-59925087	HCT-116	colon:	n/a
48	chr12:59925323-59925373	AG10803	skin:	n/a
49	chr12:59925323-59925373	HCF	heart:	n/a
50	chr12:59925323-59925373	H1-hESC	embryonic stem cell:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr12:59919709..59922642-chr12:59929595..59932355,2	MCF-7	breast:
2	chr12:59914091..59917711-chr12:59989940..59992108,3	MCF-7	breast:
3	chr12:59941726..59943985-chr12:59989663..59991635,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266724	TF binding region
ENSG00000265430	TF binding region
ENSG00000257230	TF binding region
ENSG00000266724	CpG island
ENSG00000265430	CpG island
ENSG00000257230	CpG island
ENSG00000265430	chromatin interactions
ENSG00000266724	chromatin interactions
ENSG00000118596	chromatin interactions

Extended variants
information (count: 402 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:402 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs420644	chr12:59916767-59916768	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs550533189	chr12:59916770-59916771	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs569521532	chr12:59916807-59916808	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs11173067	chr12:59916822-59916823	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs544330307	chr12:59916853-59916854	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs79106777	chr12:59916875-59916876	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs563905308	chr12:59916901-59916902	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs192584305	chr12:59916928-59916929	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs571895956	chr12:59916935-59916936	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs539231883	chr12:59916969-59916970	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs184214205	chr12:59917021-59917022	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs189582809	chr12:59917022-59917023	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs12580155	chr12:59917023-59917024	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs77370077	chr12:59917056-59917057	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs576345886	chr12:59917077-59917078	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs12580166	chr12:59917126-59917127	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs558429248	chr12:59917200-59917201	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs539051826	chr12:59917206-59917207	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs558966342	chr12:59917256-59917257	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs576670991	chr12:59917317-59917318	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs540834058	chr12:59917353-59917354	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs529197434	chr12:59917355-59917356	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs559072388	chr12:59917374-59917375	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs181240106	chr12:59917401-59917402	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs541524154	chr12:59917409-59917410	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs372638204	chr12:59917410-59917411	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs548893976	chr12:59917422-59917423	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs530403092	chr12:59917451-59917452	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs562735024	chr12:59917504-59917505	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs550541629	chr12:59917571-59917572	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs186751513	chr12:59917589-59917590	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs538321782	chr12:59917604-59917605	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs368050422	chr12:59917648-59917649	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs143467865	chr12:59917662-59917663	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs574980562	chr12:59917746-59917747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs371232764	chr12:59917764-59917765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs540386408	chr12:59917792-59917793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs548032728	chr12:59917837-59917838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs276011	chr12:59917913-59917914	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs536789361	chr12:59917966-59917967	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs554745336	chr12:59918011-59918012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs117693415	chr12:59918035-59918036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs537040633	chr12:59918062-59918063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs146745903	chr12:59918071-59918072	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs576726376	chr12:59918084-59918085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs12369542	chr12:59918266-59918267	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs188683059	chr12:59918289-59918290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs181466319	chr12:59918290-59918291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs567263700	chr12:59918315-59918316	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs35144080	chr12:59918316-59918317	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

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
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
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
Urothelial cell carcinoma	18451213	CNVD
Melanoma	18172304	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
Glioblastoma multiforme	20080666	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	17133270	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Glioblastoma	17090523	CNVD
Multiple myeloma	16616336	CNVD
Lung cancer	16773561	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59912400-59921000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59942000-59943600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:59942200-59943800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:59942400-59943200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr12:59942400-59943200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr12:59942600-59943000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:59942600-59943200	Enhancers	Stomach Mucosa	stomach
8	chr12:59942600-59943400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:59942600-59943600	Enhancers	Esophagus	oesophagus
10	chr12:59942600-59944000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:59943000-59943200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:59943200-59943400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr12:59943200-59943600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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