Variant report

Variant	esv3379602
Chromosome Location	chr12:123179885-123191721
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	chr12:123184951-123185203	GM12878	blood:	n/a	n/a
2	BATF	chr12:123184904-123185288	GM12878	blood:	n/a	n/a
3	BCL11A	chr12:123184925-123185178	GM12878	blood:	n/a	chr12:123185140-123185149
4	CEBPB	chr12:123187833-123188233	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr12:123187794-123188089	HepG2	liver:	n/a	n/a
6	CEBPB	chr12:123187869-123188146	A549	lung:	n/a	n/a
7	E2F4	chr12:123187896-123188134	MCF10A-Er-Src	breast:	n/a	n/a
8	EBF1	chr12:123187949-123188264	GM12878	blood:	n/a	n/a
9	EBF1	chr12:123187913-123188259	GM12878	blood:	n/a	n/a
10	EP300	chr12:123187789-123188123	HepG2	liver:	n/a	n/a
11	FOS	chr12:123187706-123188305	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr12:123187821-123188180	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr12:123187796-123188158	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr12:123187570-123188311	MCF10A-Er-Src	breast:	n/a	n/a
15	FOSL2	chr12:123184573-123184941	HepG2	liver:	n/a	chr12:123184777-123184784 chr12:123184772-123184783 chr12:123184772-123184784 chr12:123184774-123184782
16	FOSL2	chr12:123180453-123180796	HepG2	liver:	n/a	n/a
17	FOXA1	chr12:123187806-123188302	HepG2	liver:	n/a	n/a
18	FOXA1	chr12:123187829-123188220	HepG2	liver:	n/a	n/a
19	FOXA2	chr12:123187936-123188118	HepG2	liver:	n/a	n/a
20	HEY1	chr12:123187714-123188013	HepG2	liver:	n/a	n/a
21	IRF4	chr12:123184845-123185339	GM12878	blood:	n/a	n/a
22	IRF4	chr12:123184590-123185349	GM12878	blood:	n/a	n/a
23	JUND	chr12:123184699-123184834	HepG2	liver:	n/a	chr12:123184777-123184784 chr12:123184772-123184783 chr12:123184772-123184784 chr12:123184774-123184782
24	JUND	chr12:123184677-123184863	HepG2	liver:	n/a	chr12:123184777-123184784 chr12:123184772-123184783 chr12:123184772-123184784 chr12:123184774-123184782
25	MYC	chr12:123187750-123188250	MCF10A-Er-Src	breast:	n/a	n/a
26	MYC	chr12:123187728-123188305	MCF10A-Er-Src	breast:	n/a	n/a
27	MYC	chr12:123180584-123180604	MCF-7	breast:	n/a	n/a
28	NFIC	chr12:123184737-123185315	GM12878	blood:	n/a	n/a
29	PAX5	chr12:123184834-123185208	GM12878	blood:	n/a	chr12:123185140-123185149
30	POLR2A	chr12:123186413-123186760	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr12:123187655-123188092	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:123180475-123180685	MCF-7	breast:	n/a	n/a
33	POLR2A	chr12:123185972-123186119	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr12:123186895-123186998	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr12:123187757-123187873	HepG2	liver:	n/a	n/a
36	POLR2A	chr12:123187462-123188263	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr12:123180462-123180472	MCF-7	breast:	n/a	n/a
38	POLR2A	chr12:123180690-123180797	MCF-7	breast:	n/a	n/a
39	POLR2A	chr12:123180215-123180345	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:123187704-123188015	Hela-S3	cervix:	n/a	n/a
41	POU2F2	chr12:123187839-123188275	GM12878	blood:	n/a	n/a
42	POU2F2	chr12:123188001-123188214	GM12878	blood:	n/a	n/a
43	SP1	chr12:123184902-123185193	GM12878	blood:	n/a	n/a
44	SP1	chr12:123180285-123180786	HepG2	liver:	n/a	n/a
45	SP1	chr12:123184917-123185192	GM12878	blood:	n/a	n/a
46	SPI1	chr12:123185014-123185250	GM12878	blood:	n/a	chr12:123185169-123185182 chr12:123185140-123185149
47	SPI1	chr12:123184645-123185493	GM12878	blood:	n/a	chr12:123184835-123184842 chr12:123185169-123185182 chr12:123185140-123185149
48	SPI1	chr12:123182350-123182587	GM12878	blood:	n/a	chr12:123182479-123182492 chr12:123182481-123182488 chr12:123182473-123182486 chr12:123182475-123182482
49	SPI1	chr12:123184653-123185305	GM12878	blood:	n/a	chr12:123184835-123184842 chr12:123185169-123185182 chr12:123185140-123185149
50	SPI1	chr12:123184707-123185335	GM12891	blood:	n/a	chr12:123184835-123184842 chr12:123185169-123185182 chr12:123185140-123185149

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123187529-123187579	AG04449	skin:	fetal
2	chr12:123187529-123187579	AG04449	skin:	fetal
3	chr12:123189236-123189286	SK-N-SH_RA	brain:	n/a
4	chr12:123188078-123188128	HIPEpiC	eye:	n/a
5	chr12:123188078-123188128	T-47D	breast:	n/a
6	chr12:123187474-123187524	GM06990	blood:	n/a
7	chr12:123188078-123188128	HEK293	kidney:	embryo
8	chr12:123189236-123189286	HCM	heart:	n/a
9	chr12:123187474-123187524	MCF10A-Er-Src	breast:	n/a
10	chr12:123188078-123188128	NH-A	brain:	n/a
11	chr12:123189256-123189306	Hela-S3	cervix:	n/a
12	chr12:123187474-123187524	GM12891	blood:	n/a
13	chr12:123188078-123188128	A549	lung:	n/a
14	chr12:123188078-123188128	HRE	kidney:	n/a
15	chr12:123189256-123189306	A549	lung:	n/a
16	chr12:123187529-123187579	Hepatocyte	liver:	n/a
17	chr12:123187529-123187579	HCPEpiC	choroid plexus:	n/a
18	chr12:123189236-123189286	GM12892	blood:	n/a
19	chr12:123188078-123188128	SK-N-MC	brain:	n/a
20	chr12:123187529-123187579	AoSMC	blood vessel:	n/a
21	chr12:123189256-123189306	HMEC	breast:	n/a
22	chr12:123187529-123187579	NHDF-neo	bronchial:	n/a
23	chr12:123187529-123187579	Hela-S3	cervix:	n/a
24	chr12:123187073-123187123	AG09319	gingival:	n/a
25	chr12:123189256-123189306	SAEC	small airway:	n/a
26	chr12:123187073-123187123	GM12891	blood:	n/a
27	chr12:123188078-123188128	Hepatocyte	liver:	n/a
28	chr12:123187529-123187579	ProgFib	skin:	n/a
29	chr12:123187474-123187524	AG09309	skin:	n/a
30	chr12:123189256-123189306	Caco-2	colon:	n/a
31	chr12:123187073-123187123	MCF-7	breast:	n/a
32	chr12:123188078-123188128	BJ	skin:	n/a
33	chr12:123189236-123189286	HCPEpiC	choroid plexus:	n/a
34	chr12:123187073-123187123	NT2-D1	testis:	n/a
35	chr12:123189256-123189306	SK-N-MC	brain:	n/a
36	chr12:123189256-123189306	ProgFib	skin:	n/a
37	chr12:123187073-123187123	ProgFib	skin:	n/a
38	chr12:123188078-123188128	ProgFib	skin:	n/a
39	chr12:123189256-123189306	ECC-1	luminal epithelium:	n/a
40	chr12:123187073-123187123	T-47D	breast:	n/a
41	chr12:123187474-123187524	MCF-7	breast:	n/a
42	chr12:123187073-123187123	H1-hESC	embryonic stem cell:	embryo
43	chr12:123188078-123188128	U87	brain:	n/a
44	chr12:123189236-123189286	HCT-116	colon:	n/a
45	chr12:123188078-123188128	AG04449	skin:	fetal
46	chr12:123189256-123189306	AG09319	gingival:	n/a
47	chr12:123187474-123187524	HCF	heart:	n/a
48	chr12:123189256-123189306	AG10803	skin:	n/a
49	chr12:123187073-123187123	MCF10A-Er-Src	breast:	n/a
50	chr12:123187529-123187579	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123171777..123173769-chr12:123177481..123180099,2	MCF-7	breast:
2	chr12:123186486..123188573-chr12:123199930..123201817,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DENR-2	chr12:123185843-123186416	NONHSAT031529

Variant related genes	Relation type
HCAR2	TF binding region
HCAR2	CpG island
ENSG00000255398	chromatin interactions

Extended variants
information (count: 657 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:657 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs193211495	chr12:123179888-123179889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs138124048	chr12:123180005-123180006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs528644878	chr12:123180016-123180017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs1798219	chr12:123180061-123180062	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs534622916	chr12:123180063-123180064	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs552981184	chr12:123180088-123180089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs571866734	chr12:123180095-123180096	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs185560822	chr12:123180097-123180098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs556923185	chr12:123180116-123180117	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs2454723	chr12:123180119-123180120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs575399989	chr12:123180140-123180141	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs374655961	chr12:123180151-123180152	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs199498854	chr12:123180197-123180198	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs6489208	chr12:123180224-123180225	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs6489209	chr12:123180226-123180227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs6489210	chr12:123180245-123180246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs369682326	chr12:123180254-123180255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs2264446	chr12:123180255-123180256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs7299398	chr12:123180260-123180261	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs7134798	chr12:123180266-123180267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs567241713	chr12:123180267-123180268	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs7134802	chr12:123180276-123180277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs530330055	chr12:123180325-123180326	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs548464595	chr12:123180333-123180334	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs541204336	chr12:123180354-123180355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs368080230	chr12:123180355-123180356	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs373793819	chr12:123180356-123180357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs200230649	chr12:123180380-123180381	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs111951562	chr12:123180449-123180450	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs534691929	chr12:123180465-123180466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs372015430	chr12:123180469-123180470	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs61955023	chr12:123180666-123180667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs12370672	chr12:123180904-123180905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs533855872	chr12:123180982-123180983	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs545417498	chr12:123180991-123180992	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs571260221	chr12:123180993-123180994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs538210965	chr12:123181020-123181021	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs557233494	chr12:123181100-123181101	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs1798183	chr12:123181193-123181194	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs1696337	chr12:123181211-123181212	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs1696338	chr12:123181212-123181213	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs150852616	chr12:123181233-123181234	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs536471619	chr12:123181249-123181250	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs201141024	chr12:123181279-123181280	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs601949	chr12:123181284-123181285	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs71440205	chr12:123181427-123181428	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs544251765	chr12:123181444-123181445	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs71085839	chr12:123181455-123181456	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs554323094	chr12:123181459-123181460	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs573038032	chr12:123181493-123181494	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:68)

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
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
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	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
lymphocytic leukemia	21291569	CNVD
Breast cancer	16397240	CNVD
Breast cancer	17133270	CNVD
Breast cancer	17603634	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Schizophrenia	18923514	CNVD
Schizophrenia	22241247	CNVD
Cryptorchidism	21048976	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Neuroblastoma	18923191	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	21806811	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Beckwith-Wiedemann syndrome	20648245	CNVD
Developmental delay	21457577	CNVD
dysmorphic	21457577	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Olfactory neuroblastoma	18408657	CNVD
Chordoma	18071362	CNVD

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123166600-123187800	Weak transcription	A549	lung
2	chr12:123174000-123199800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:123176400-123182000	Weak transcription	Adipose Nuclei	Adipose
4	chr12:123176400-123182400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:123178200-123181000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:123180600-123182400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:123181000-123181800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:123181200-123182200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:123181200-123182400	Enhancers	Placenta	Placenta
10	chr12:123181200-123183000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:123181200-123183000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:123181600-123182600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr12:123181600-123182600	Enhancers	HMEC	breast
14	chr12:123181600-123182600	Enhancers	NHEK	skin
15	chr12:123181800-123185400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:123182000-123182600	Enhancers	Adipose Nuclei	Adipose
17	chr12:123182200-123184200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:123182400-123182600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr12:123182400-123182800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:123182400-123182800	Weak transcription	Placenta	Placenta
21	chr12:123182400-123183000	Enhancers	Primary T cells from cord blood	blood
22	chr12:123182600-123183800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr12:123182600-123185200	Weak transcription	Adipose Nuclei	Adipose
24	chr12:123182600-123185200	Weak transcription	HMEC	breast
25	chr12:123182600-123185400	Weak transcription	NHEK	skin
26	chr12:123182800-123183000	Enhancers	Placenta	Placenta
27	chr12:123182800-123185200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:123183000-123185000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:123183000-123185200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:123183000-123185400	Weak transcription	Placenta	Placenta
31	chr12:123183800-123184800	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr12:123184000-123188800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:123184200-123185800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:123184800-123185200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:123185000-123185400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:123185200-123185400	Active TSS	Adipose Nuclei	Adipose
37	chr12:123185200-123185800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:123185200-123186000	Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr12:123185200-123186000	Enhancers	HMEC	breast
40	chr12:123185200-123186000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:123185200-123187200	Active TSS	Esophagus	oesophagus
42	chr12:123185400-123185600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:123185400-123185600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:123185400-123185600	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr12:123185400-123185600	Enhancers	Placenta	Placenta
46	chr12:123185400-123185600	Flanking Active TSS	NHEK	skin
47	chr12:123185400-123186200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:123185400-123186800	Active TSS	Primary hematopoietic stem cells	blood
49	chr12:123185400-123188200	Active TSS	Primary B cells from cord blood	blood
50	chr12:123185600-123185800	Active TSS	Adipose Nuclei	Adipose

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