Variant report

Variant	esv3368352
Chromosome Location	chr12:48883189-48883540
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	BATF	chr12:48882829-48883217	GM12878	blood:	n/a	chr12:48883023-48883034
2	BCL11A	chr12:48882852-48883267	GM12878	blood:	n/a	n/a
3	BCLAF1	chr12:48882751-48883247	GM12878	blood:	n/a	n/a
4	BHLHE40	chr12:48882898-48883195	GM12878	blood:	n/a	n/a
5	CEBPB	chr12:48882593-48883325	GM12878	blood:	n/a	n/a
6	E2F4	chr12:48882935-48883203	MCF10A-Er-Src	breast:	n/a	n/a
7	EBF1	chr12:48882732-48883206	GM12878	blood:	n/a	chr12:48882931-48882942
8	EP300	chr12:48882814-48883236	GM12878	blood:	n/a	n/a
9	EP300	chr12:48882788-48883206	GM12878	blood:	n/a	n/a
10	FOS	chr12:48882762-48883225	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr12:48882825-48883232	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr12:48882823-48883213	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr12:48882837-48883421	MCF10A-Er-Src	breast:	n/a	n/a
14	FOXM1	chr12:48882633-48883283	GM12878	blood:	n/a	n/a
15	IRF4	chr12:48882807-48883262	GM12878	blood:	n/a	n/a
16	MYC	chr12:48882797-48883582	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr12:48882824-48883500	MCF10A-Er-Src	breast:	n/a	n/a
18	NFIC	chr12:48882423-48883336	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:48882749-48883524	MCF10A-Er-Src	breast:	n/a	n/a
20	RUNX3	chr12:48882700-48883303	GM12878	blood:	n/a	n/a
21	RUNX3	chr12:48882835-48883231	GM12878	blood:	n/a	n/a
22	SP1	chr12:48882789-48883194	GM12878	blood:	n/a	n/a
23	SRF	chr12:48882885-48883223	GM12878	blood:	n/a	chr12:48883067-48883080 chr12:48883069-48883078 chr12:48883068-48883082 chr12:48883068-48883079
24	SRF	chr12:48882914-48883195	GM12878	blood:	n/a	chr12:48883067-48883080 chr12:48883069-48883078 chr12:48883068-48883082 chr12:48883068-48883079
25	STAT3	chr12:48882800-48883232	MCF10A-Er-Src	breast:	n/a	n/a
26	STAT3	chr12:48882896-48883206	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr12:48882822-48883227	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr12:48882896-48883192	GM12878	blood:	n/a	n/a
29	TBP	chr12:48882671-48883205	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48880500..48882865-chr12:48883478..48886344,3	K562	blood:
2	chr12:48882871..48884702-chr12:48885100..48887755,2	K562	blood:

Variant related genes	Relation type
C12orf54	TF binding region
ENSG00000240443	chromatin interactions
ENSG00000177627	chromatin interactions

Extended variants
information (count: 19 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200739829	chr12:48883208-48883209	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs370397633	chr12:48883209-48883210	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs56968979	chr12:48883225-48883226	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs182756388	chr12:48883287-48883288	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs35342454	chr12:48883301-48883302	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs548974799	chr12:48883302-48883303	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs140377696	chr12:48883308-48883309	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs2731097	chr12:48883311-48883312	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs556347734	chr12:48883342-48883343	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs537974979	chr12:48883381-48883382	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs576162553	chr12:48883396-48883397	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs188122959	chr12:48883406-48883407	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs555542939	chr12:48883464-48883465	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs2731098	chr12:48883468-48883469	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs377197542	chr12:48883469-48883470	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs556288206	chr12:48883485-48883486	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs189981274	chr12:48883492-48883493	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs550607081	chr12:48883508-48883509	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs34855520	chr12:48883509-48883510	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:68)

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
Breast cancer	22522925	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48881600-48883800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48881600-48884000	Enhancers	HMEC	breast
3	chr12:48882400-48884000	Enhancers	GM12878-XiMat	blood
4	chr12:48882600-48883600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:48882800-48883200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:48882800-48883400	Flanking Active TSS	NHEK	skin
7	chr12:48883000-48883200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:48883200-48884000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:48883400-48884000	Enhancers	NHEK	skin

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