Variant report

Variant	esv3408844
Chromosome Location	chr12:104607310-104607778
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	EP300	chr12:104607719-104608272	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr12:104607628-104608286	SK-N-SH	brain:	n/a	n/a
3	EP300	chr12:104607661-104607960	T-47D	breast:	n/a	n/a
4	EP300	chr12:104607734-104608242	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr12:104607630-104608104	T-47D	breast:	n/a	n/a
6	EP300	chr12:104607550-104608143	A549	lung:	n/a	n/a
7	EP300	chr12:104607549-104608283	A549	lung:	n/a	n/a
8	ESR1	chr12:104607662-104607972	T-47D	breast:	n/a	n/a
9	ESR1	chr12:104607614-104608002	T-47D	breast:	n/a	n/a
10	ESR1	chr12:104607644-104608057	T-47D	breast:	n/a	n/a
11	ESR1	chr12:104607703-104607988	T-47D	breast:	n/a	n/a
12	FOSL2	chr12:104607558-104608362	A549	lung:	n/a	n/a
13	FOSL2	chr12:104607718-104608254	SK-N-SH	brain:	n/a	n/a
14	FOXA1	chr12:104607644-104607937	HepG2	liver:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
15	FOXA1	chr12:104607702-104608014	T-47D	breast:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
16	FOXA1	chr12:104607546-104608017	T-47D	breast:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
17	FOXA2	chr12:104607486-104608174	A549	lung:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
18	FOXA2	chr12:104607493-104608080	A549	lung:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
19	GATA3	chr12:104607648-104608413	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr12:104607642-104608130	T-47D	breast:	n/a	n/a
21	GATA3	chr12:104607552-104608198	A549	lung:	n/a	n/a
22	GATA3	chr12:104607705-104608229	SK-N-SH	brain:	n/a	n/a
23	JUND	chr12:104607663-104608119	A549	lung:	n/a	n/a
24	MAX	chr12:104607727-104608159	SK-N-SH	brain:	n/a	n/a
25	MAX	chr12:104607741-104608140	SK-N-SH	brain:	n/a	n/a
26	NFIC	chr12:104607662-104608326	SK-N-SH	brain:	n/a	n/a
27	PBX3	chr12:104607649-104608216	SK-N-SH	brain:	n/a	n/a
28	PBX3	chr12:104607698-104608339	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr12:104607579-104608308	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr12:104607712-104608039	U87	brain:	n/a	n/a
31	POLR2A	chr12:104607656-104608212	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr12:104607603-104608153	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr12:104607749-104608142	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr12:104607677-104608039	U87	brain:	n/a	n/a
35	POLR2A	chr12:104607561-104608156	PANC-1	pancreas:	n/a	n/a
36	RAD21	chr12:104607732-104608090	SK-N-SH_RA	brain:	n/a	n/a
37	RAD21	chr12:104607727-104608100	SK-N-SH_RA	brain:	n/a	n/a
38	RCOR1	chr12:104607564-104608232	IMR90	lung:	n/a	n/a
39	REST	chr12:104607739-104608037	PANC-1	pancreas:	n/a	n/a
40	REST	chr12:104607545-104608145	A549	lung:	n/a	n/a
41	REST	chr12:104607775-104607998	SK-N-SH	brain:	n/a	n/a
42	REST	chr12:104607638-104608121	PFSK-1	brain:	n/a	n/a
43	REST	chr12:104607675-104608078	PFSK-1	brain:	n/a	n/a
44	SIN3AK20	chr12:104607726-104608024	PFSK-1	brain:	n/a	n/a
45	SIN3AK20	chr12:104607763-104608107	PFSK-1	brain:	n/a	n/a
46	SP1	chr12:104607564-104608334	A549	lung:	n/a	n/a
47	SP1	chr12:104607540-104608232	A549	lung:	n/a	n/a
48	TCF12	chr12:104607409-104608582	A549	lung:	n/a	chr12:104608377-104608387
49	TCF12	chr12:104607631-104608498	SK-N-SH	brain:	n/a	chr12:104608377-104608387
50	TCF12	chr12:104607532-104608483	SK-N-SH	brain:	n/a	chr12:104608377-104608387

No.	Distal block	Cell Line	Cell type
1	chr12:104606650..104611349-chr12:104679680..104683932,8	K562	blood:
2	chr12:104606513..104608916-chr12:104687474..104689999,2	K562	blood:
3	chr12:104605545..104609502-chr12:104611890..104614832,4	MCF-7	breast:
4	chr12:104529918..104532327-chr12:104605294..104607957,2	MCF-7	breast:
5	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000198431	chromatin interactions
ENSG00000120837	chromatin interactions

Extended variants
information (count: 21 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs371968657	chr12:104607315-104607316	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs143714511	chr12:104607364-104607365	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs199704504	chr12:104607365-104607366	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs549583764	chr12:104607367-104607368	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs560858826	chr12:104607404-104607405	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs563973316	chr12:104607414-104607415	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs182642346	chr12:104607429-104607430	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs546042558	chr12:104607432-104607433	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs141828340	chr12:104607433-104607434	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs368103651	chr12:104607438-104607439	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs537649827	chr12:104607439-104607440	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs35724875	chr12:104607453-104607454	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs187678048	chr12:104607480-104607481	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs192726726	chr12:104607538-104607539	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs72487512	chr12:104607580-104607581	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs541567251	chr12:104607581-104607582	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs532619210	chr12:104607624-104607625	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs552406984	chr12:104607632-104607633	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs140747866	chr12:104607633-104607634	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs184132972	chr12:104607688-104607689	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs367625394	chr12:104607709-104607710	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
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
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	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
Lung cancer	18438408	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	22032731	CNVD
Cancer	16751803	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
lymphocytic leukemia	21291569	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16397240	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	17133270	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Neurocytoma	17123091	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104599200-104609200	Weak transcription	Ovary	ovary
2	chr12:104602000-104609200	Weak transcription	HSMM	muscle
3	chr12:104605200-104607800	Weak transcription	NHDF-Ad	bronchial
4	chr12:104606400-104607800	Enhancers	A549	lung
5	chr12:104606600-104607400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:104606800-104607800	Weak transcription	Osteobl	bone
7	chr12:104607000-104609200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:104607400-104607800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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