Variant report

Variant	esv3511339
Chromosome Location	chr12:1923022-1925559
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	ARID3A	chr12:1925448-1925599	HepG2	liver:	n/a	n/a
2	CEBPB	chr12:1925053-1925265	IMR90	lung:	n/a	chr12:1925179-1925190
3	CEBPB	chr12:1925068-1925245	K562	blood:	n/a	chr12:1925179-1925190
4	CEBPB	chr12:1925092-1925284	HepG2	liver:	n/a	chr12:1925179-1925190
5	CEBPB	chr12:1925008-1925361	HepG2	liver:	n/a	chr12:1925179-1925190
6	EP300	chr12:1924947-1925773	HepG2	liver:	n/a	n/a
7	EP300	chr12:1925149-1925618	HepG2	liver:	n/a	n/a
8	EP300	chr12:1925248-1925769	HepG2	liver:	n/a	n/a
9	FOS	chr12:1925053-1925328	MCF10A-Er-Src	breast:	n/a	chr12:1925131-1925142
10	FOS	chr12:1925104-1925186	MCF10A-Er-Src	breast:	n/a	chr12:1925131-1925142
11	FOS	chr12:1925021-1925280	MCF10A-Er-Src	breast:	n/a	chr12:1925131-1925142
12	FOSL2	chr12:1924926-1925802	HepG2	liver:	n/a	chr12:1925131-1925142
13	FOXA1	chr12:1925000-1925687	HepG2	liver:	n/a	n/a
14	FOXA2	chr12:1925007-1925289	HepG2	liver:	n/a	n/a
15	GATA2	chr12:1924324-1924546	SH-SY5Y	brain:	n/a	n/a
16	GATA3	chr12:1923455-1923775	MCF-7	breast:	n/a	n/a
17	HDAC2	chr12:1925410-1925788	HepG2	liver:	n/a	n/a
18	HNF4A	chr12:1925331-1925735	HepG2	liver:	n/a	chr12:1925542-1925555 chr12:1925540-1925555 chr12:1925541-1925555
19	HNF4A	chr12:1925354-1925799	HepG2	liver:	n/a	chr12:1925542-1925555 chr12:1925540-1925555 chr12:1925541-1925555
20	HNF4G	chr12:1925333-1925828	HepG2	liver:	n/a	chr12:1925542-1925555 chr12:1925541-1925555 chr12:1925541-1925556
21	JUN	chr12:1921789-1923042	K562	blood:	n/a	chr12:1921946-1921957
22	MBD4	chr12:1925424-1926119	HepG2	liver:	n/a	n/a
23	MYBL2	chr12:1925085-1925777	HepG2	liver:	n/a	n/a
24	MYBL2	chr12:1925310-1925864	HepG2	liver:	n/a	n/a
25	MYC	chr12:1925496-1925543	HepG2	liver:	n/a	n/a
26	MYC	chr12:1925545-1925559	HepG2	liver:	n/a	n/a
27	NFIC	chr12:1925446-1925741	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:1923064-1923100	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr12:1925553-1926132	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr12:1925544-1926140	H1-neurons	neurons:	n/a	n/a
31	RCOR1	chr12:1924438-1924638	K562	blood:	n/a	n/a
32	RCOR1	chr12:1925526-1925955	HepG2	liver:	n/a	n/a
33	REST	chr12:1925079-1926221	H1-neurons	neurons:	n/a	chr12:1925852-1925872
34	RXRA	chr12:1925385-1925775	HepG2	liver:	n/a	chr12:1925540-1925556
35	SP1	chr12:1925018-1926128	HepG2	liver:	n/a	n/a
36	TAL1	chr12:1924531-1924603	K562	blood:	n/a	n/a
37	TBP	chr12:1925183-1925480	HepG2	liver:	n/a	n/a
38	ZNF263	chr12:1925164-1925516	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1921269..1923557-chr12:2112437..2115050,2	MCF-7	breast:
2	chr12:1923170..1923815-chr12:2041317..2042058,2	MCF-7	breast:
3	chr12:1923163..1923961-chr12:1939620..1940160,2	MCF-7	breast:
4	chr12:1923066..1926339-chr12:1927484..1932040,5	MCF-7	breast:
5	chr12:1915615..1917986-chr12:1924786..1926838,2	K562	blood:
6	chr12:1925102..1928805-chr12:1946979..1949915,3	MCF-7	breast:
7	chr12:1923072..1925795-chr12:1938699..1940589,2	MCF-7	breast:
8	chr12:1923170..1924049-chr12:2041180..2042060,3	MCF-7	breast:

Variant related genes	Relation type
CACNA2D4	TF binding region
LRTM2	TF binding region
ENSG00000203593	chromatin interactions
ENSG00000166159	chromatin interactions
ENSG00000151065	chromatin interactions

Extended variants
information (count: 110 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:110 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs192151895	chr12:1923023-1923024	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs12578700	chr12:1923040-1923041	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs184541479	chr12:1923086-1923087	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs573947641	chr12:1923106-1923107	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs190386839	chr12:1923117-1923118	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs562707228	chr12:1923118-1923119	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs533333389	chr12:1923138-1923139	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs548504619	chr12:1923140-1923141	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs78614635	chr12:1923211-1923212	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs193302273	chr12:1923218-1923219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs149636532	chr12:1923245-1923246	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs559682482	chr12:1923248-1923249	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs549061467	chr12:1923250-1923251	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs184322852	chr12:1923259-1923260	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs189600003	chr12:1923269-1923270	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs144405852	chr12:1923281-1923282	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs369000171	chr12:1923285-1923286	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs538450139	chr12:1923337-1923338	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs181192848	chr12:1923397-1923398	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs35512532	chr12:1923415-1923416	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs555043501	chr12:1923427-1923428	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs185790032	chr12:1923430-1923431	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs371559363	chr12:1923462-1923463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs373973289	chr12:1923485-1923486	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs188940546	chr12:1923500-1923501	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs376398070	chr12:1923523-1923524	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs544538736	chr12:1923524-1923525	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs369160398	chr12:1923533-1923534	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs148395737	chr12:1923543-1923544	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs142370151	chr12:1923569-1923570	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs530175938	chr12:1923582-1923583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs573413684	chr12:1923583-1923584	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs545231429	chr12:1923591-1923592	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs181631751	chr12:1923622-1923623	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs76603393	chr12:1923626-1923627	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs187204088	chr12:1923675-1923676	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs77652909	chr12:1923694-1923695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs531719241	chr12:1923700-1923701	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs550148824	chr12:1923714-1923715	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs139868343	chr12:1923812-1923813	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs532342097	chr12:1923813-1923814	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs116272505	chr12:1923814-1923815	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs565788294	chr12:1923826-1923827	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs535932074	chr12:1923842-1923843	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs115575913	chr12:1923847-1923848	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs569869108	chr12:1923848-1923849	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs143321923	chr12:1923852-1923853	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs79019277	chr12:1923853-1923854	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs191932662	chr12:1923872-1923873	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs549473177	chr12:1923883-1923884	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Glaucoma	21310917	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Squamous cell cancer	19607727	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Mental retardation	17847001	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
abnormal development	18461090	CNVD
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	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
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21509527	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Ovarian cancer	21720365	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1905600-1928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:1918200-1924000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr12:1918800-1924000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:1919200-1924000	Enhancers	Adipose Nuclei	Adipose
5	chr12:1919800-1926000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:1920000-1925600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:1920000-1939400	Weak transcription	Gastric	stomach
8	chr12:1920200-1923600	Enhancers	Placenta	Placenta
9	chr12:1920600-1923400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr12:1921000-1923800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:1921200-1925400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:1921400-1925400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:1921600-1923200	Bivalent Enhancer	NHDF-Ad	bronchial
14	chr12:1921800-1923800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:1922200-1923200	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:1922400-1923200	Enhancers	Primary B cells from cord blood	blood
17	chr12:1922400-1923600	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr12:1922600-1925000	Weak transcription	Fetal Intestine Small	intestine
19	chr12:1922600-1925000	Enhancers	HepG2	liver
20	chr12:1922600-1925400	Weak transcription	Fetal Thymus	thymus
21	chr12:1922600-1925800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:1922800-1923200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:1923000-1923200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
24	chr12:1923000-1923800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr12:1923200-1923600	Enhancers	Duodenum Mucosa	Duodenum
26	chr12:1923200-1924000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:1923400-1924000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr12:1924000-1925600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr12:1924800-1926600	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr12:1925000-1926200	Enhancers	Fetal Intestine Small	intestine
31	chr12:1925000-1926200	Flanking Active TSS	HepG2	liver
32	chr12:1925200-1925400	Enhancers	Fetal Heart	heart
33	chr12:1925200-1925400	Bivalent Enhancer	Fetal Intestine Large	intestine
34	chr12:1925200-1925800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:1925400-1925600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:1925400-1925800	Enhancers	Fetal Intestine Large	intestine
37	chr12:1925400-1925800	Enhancers	Fetal Thymus	thymus
38	chr12:1925400-1926000	Bivalent Enhancer	Placenta	Placenta
39	chr12:1925400-1926200	Bivalent Enhancer	Fetal Heart	heart

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