Variant report

Variant	esv3502241
Chromosome Location	chr12:58458223-58490223
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	chr12:58479834-58480082	GM12878	blood:	n/a	chr12:58479989-58480000
2	BHLHE40	chr12:58481302-58481476	K562	blood:	n/a	n/a
3	BRCA1	chr12:58475354-58475627	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr12:58462717-58462726	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr12:58484281-58484493	K562	blood:	n/a	chr12:58484304-58484317 chr12:58484402-58484413
6	CEBPB	chr12:58463277-58463821	Hela-S3	cervix:	n/a	chr12:58463488-58463505 chr12:58463491-58463502
7	CEBPB	chr12:58475293-58475738	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr12:58463258-58463716	ECC-1	luminal epithelium:	n/a	chr12:58463488-58463505 chr12:58463491-58463502
9	CEBPB	chr12:58463415-58463530	HepG2	liver:	n/a	chr12:58463488-58463505 chr12:58463491-58463502
10	CEBPB	chr12:58484256-58484587	A549	lung:	n/a	chr12:58484304-58484317 chr12:58484402-58484413
11	CEBPB	chr12:58458560-58458698	Hela-S3	cervix:	n/a	chr12:58458655-58458668
12	CEBPB	chr12:58461271-58461821	MCF-7	breast:	n/a	n/a
13	CEBPB	chr12:58461290-58461883	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr12:58463252-58463732	ECC-1	luminal epithelium:	n/a	chr12:58463488-58463505 chr12:58463491-58463502
15	CEBPB	chr12:58461252-58461900	MCF-7	breast:	n/a	n/a
16	CEBPB	chr12:58484281-58484518	IMR90	lung:	n/a	chr12:58484304-58484317 chr12:58484402-58484413
17	CEBPB	chr12:58484294-58484531	HepG2	liver:	n/a	chr12:58484304-58484317 chr12:58484402-58484413
18	CHD2	chr12:58461371-58461841	Hela-S3	cervix:	n/a	n/a
19	CHD2	chr12:58475308-58475626	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr12:58480880-58481030	GM12867	blood:	n/a	n/a
21	CTCF	chr12:58488460-58488610	GM12878	blood:	n/a	n/a
22	CTCF	chr12:58475540-58475690	HCT-116	colon:	n/a	n/a
23	CTCF	chr12:58461900-58462050	MCF-7	breast:	n/a	n/a
24	CTCF	chr12:58483700-58483850	GM12866	blood:	n/a	n/a
25	CTCF	chr12:58475540-58475690	MCF-7	breast:	n/a	n/a
26	CTCF	chr12:58475534-58475640	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr12:58484520-58484670	NHDF-neo	bronchial:	n/a	n/a
28	E2F4	chr12:58463359-58463871	MCF10A-Er-Src	breast:	n/a	chr12:58463458-58463467
29	E2F4	chr12:58461423-58461623	MCF10A-Er-Src	breast:	n/a	n/a
30	E2F6	chr12:58481199-58481852	H1-hESC	embryonic stem cell:	n/a	chr12:58481669-58481679
31	ELK1	chr12:58461299-58461740	Hela-S3	cervix:	n/a	n/a
32	EP300	chr12:58461257-58461862	T-47D	breast:	n/a	n/a
33	EP300	chr12:58475346-58475638	Hela-S3	cervix:	n/a	n/a
34	EP300	chr12:58461222-58461731	T-47D	breast:	n/a	n/a
35	EP300	chr12:58463327-58463728	Hela-S3	cervix:	n/a	chr12:58463605-58463614 chr12:58463492-58463506
36	EP300	chr12:58461316-58462011	Hela-S3	cervix:	n/a	n/a
37	ESR1	chr12:58461364-58461675	T-47D	breast:	n/a	n/a
38	ESR1	chr12:58461351-58461663	T-47D	breast:	n/a	n/a
39	FOS	chr12:58461316-58461818	MCF10A-Er-Src	breast:	n/a	n/a
40	FOS	chr12:58461316-58461836	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr12:58460133-58460478	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr12:58463356-58463620	MCF10A-Er-Src	breast:	n/a	chr12:58463508-58463516
43	FOS	chr12:58475393-58475544	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr12:58461340-58461780	Hela-S3	cervix:	n/a	n/a
45	FOS	chr12:58475416-58475615	MCF10A-Er-Src	breast:	n/a	chr12:58475539-58475549
46	FOS	chr12:58461320-58461781	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr12:58463331-58463688	MCF10A-Er-Src	breast:	n/a	chr12:58463508-58463516
48	FOS	chr12:58463337-58463682	MCF10A-Er-Src	breast:	n/a	chr12:58463508-58463516
49	FOS	chr12:58463331-58463697	MCF10A-Er-Src	breast:	n/a	chr12:58463508-58463516
50	FOS	chr12:58460179-58460415	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58460641..58463046-chr12:58464806..58468044,3	MCF-7	breast:
2	chr12:58460244..58462054-chr12:58476123..58478846,2	MCF-7	breast:
3	chr12:58427447..58430146-chr12:58459554..58461578,2	MCF-7	breast:
4	chr12:58461282..58462971-chr12:58479054..58481016,2	MCF-7	breast:
5	chr12:58469881..58471988-chr12:58473422..58476197,2	K562	blood:
6	chr12:58469881..58471988-chr12:58473422..58476197,2	K562	blood:
7	chr12:58460641..58463046-chr12:58464806..58468044,3	MCF-7	breast:
8	chr12:58471661..58473367-chr12:58475454..58477748,2	MCF-7	breast:
9	chr12:58336020..58338569-chr12:58461127..58463440,2	MCF-7	breast:
10	chr12:58460244..58462054-chr12:58476123..58478846,2	MCF-7	breast:
11	chr12:58463095..58465569-chr12:58476759..58478479,2	K562	blood:
12	chr12:58461282..58462971-chr12:58479054..58481016,2	MCF-7	breast:
13	chr12:58475657..58477578-chr12:58477868..58480225,2	MCF-7	breast:
14	chr12:58474355..58476950-chr12:58494069..58496822,2	MCF-7	breast:
15	chr12:58471661..58473367-chr12:58475454..58477748,2	MCF-7	breast:
16	chr12:58463095..58465569-chr12:58476759..58478479,2	K562	blood:
17	chr12:58475657..58477578-chr12:58477868..58480225,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-3	chr12:58483249-58483381	XLOC_010103
2	lnc-XRCC6BP1-2	chr12:58481675-58481895	ENSG00000257541.1
3	lnc-CTDSP2-4	chr12:58488695-58488894	NONHSAT029017
4	lnc-CTDSP2-4	chr12:58488697-58489622	NONHSAT029020
5	lnc-CTDSP2-3	chr12:58484638-58484682	XLOC_010103
6	lnc-XRCC6BP1-2	chr12:58482221-58482333	ENSG00000257541.1
7	lnc-CTDSP2-3	chr12:58475010-58475216	XLOC_010103
8	lnc-CTDSP2-4	chr12:58488697-58491796	ENSG00000264432.1
9	lnc-XRCC6BP1-2	chr12:58487110-58487145	ENSG00000257541.1
10	lnc-XRCC6BP1-2	chr12:58481991-58482104	ENSG00000257541.1
11	lnc-CTDSP2-4	chr12:58488696-58488894	XLOC_010104

Variant related genes	Relation type
ENSG00000257541	TF binding region
CCR9	miRNA target sites
C3orf18	miRNA target sites
MITF	miRNA target sites

Extended variants
information (count: 1163 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:1163 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556177189	chr12:58458606-58458607	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs10783873	chr12:58458623-58458624	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs182318340	chr12:58458630-58458631	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs375920624	chr12:58458676-58458677	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs575879181	chr12:58458680-58458681	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs543304950	chr12:58458685-58458686	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs565194001	chr12:58458690-58458691	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs369985947	chr12:58458718-58458719	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs61054293	chr12:58458723-58458724	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs545134032	chr12:58458732-58458733	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs186982534	chr12:58458760-58458761	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs546399904	chr12:58458778-58458779	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs190302098	chr12:58458965-58458966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs183247521	chr12:58458984-58458985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs149505343	chr12:58459000-58459001	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs143966107	chr12:58459002-58459003	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs563005923	chr12:58459021-58459022	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs111284708	chr12:58459030-58459031	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs541268687	chr12:58459031-58459032	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs982492	chr12:58459066-58459067	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs148631303	chr12:58459145-58459146	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs536342728	chr12:58459230-58459231	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs554646013	chr12:58459251-58459252	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs193028439	chr12:58459334-58459335	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs982493	chr12:58459344-58459345	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs12824706	chr12:58459408-58459409	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs577053189	chr12:58459525-58459526	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs148488926	chr12:58459532-58459533	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs541007635	chr12:58459563-58459564	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs559387258	chr12:58459617-58459618	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs142071302	chr12:58459704-58459705	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs541909209	chr12:58459709-58459710	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs563390595	chr12:58459728-58459729	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs531785508	chr12:58459738-58459739	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs184123311	chr12:58459766-58459767	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs565370067	chr12:58459822-58459823	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs111595859	chr12:58459831-58459832	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs531314916	chr12:58459832-58459833	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs376697435	chr12:58459837-58459838	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs547819173	chr12:58459868-58459869	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs2659646	chr12:58459871-58459872	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs191360855	chr12:58459897-58459898	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs548241108	chr12:58459926-58459927	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs76957538	chr12:58459947-58459948	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs34885501	chr12:58459949-58459950	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs532053049	chr12:58460004-58460005	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs567114450	chr12:58460011-58460012	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs570602340	chr12:58460031-58460032	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs375140400	chr12:58460044-58460045	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs78381902	chr12:58460070-58460071	Enhancers	n/a	n/a	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
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
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
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
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
Glioblastoma	17090523	CNVD
Multiple myeloma	16616336	CNVD
Lung cancer	16773561	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Osteosarcoma	21215367	CNVD

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58458600-58458800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:58458800-58459400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:58459000-58464400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:58459400-58461800	Enhancers	HMEC	breast
5	chr12:58459400-58464600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:58459800-58460200	Enhancers	Fetal Muscle Leg	muscle
7	chr12:58459800-58464400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:58459800-58464400	Enhancers	Hela-S3	cervix
9	chr12:58459800-58464400	Enhancers	NHEK	skin
10	chr12:58460200-58463000	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:58461200-58462000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:58461200-58462000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:58461200-58462000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:58461200-58462000	Enhancers	Pancreas	Pancrea
15	chr12:58461200-58462000	Enhancers	NH-A	brain
16	chr12:58461200-58462200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:58461200-58462200	Enhancers	Esophagus	oesophagus
18	chr12:58461600-58462200	Enhancers	Fetal Kidney	kidney
19	chr12:58461800-58462000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:58461800-58462200	Flanking Active TSS	HMEC	breast
21	chr12:58462000-58463000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:58462000-58465600	Weak transcription	Pancreas	Pancrea
23	chr12:58462200-58463000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:58462200-58463000	Weak transcription	Fetal Kidney	kidney
25	chr12:58462200-58464000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:58462200-58464400	Enhancers	HMEC	breast
27	chr12:58463000-58463200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:58463000-58463200	Enhancers	Fetal Muscle Leg	muscle
29	chr12:58463000-58463600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:58463000-58463600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr12:58463000-58463800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:58463000-58464400	Enhancers	Adipose Nuclei	Adipose
33	chr12:58463000-58464400	Enhancers	Fetal Kidney	kidney
34	chr12:58463200-58464200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:58463200-58464200	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:58463400-58463800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:58463600-58463800	Enhancers	HSMMtube	muscle
38	chr12:58463600-58464400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:58464200-58464400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:58464200-58464400	Enhancers	Fetal Muscle Leg	muscle
41	chr12:58464600-58464800	Enhancers	HSMMtube	muscle
42	chr12:58464600-58465400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:58465400-58466200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:58465600-58465800	Enhancers	Pancreas	Pancrea
45	chr12:58466200-58473600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:58469600-58469800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:58469600-58470200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:58469600-58470200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr12:58469800-58472000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:58472000-58472200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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