Variant report

Variant	esv2761733
Chromosome Location	chr12:39309714-39413045
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	chr12:39397543-39397858	HepG2	liver:	n/a	n/a
2	ARID3A	chr12:39377087-39377287	HepG2	liver:	n/a	n/a
3	BACH1	chr12:39406696-39407064	H1-hESC	embryonic stem cell:	n/a	n/a
4	BHLHE40	chr12:39313132-39313245	K562	blood:	n/a	n/a
5	CBX3	chr12:39331828-39332171	K562	blood:	n/a	n/a
6	CBX3	chr12:39331867-39332085	K562	blood:	n/a	n/a
7	CBX3	chr12:39327892-39328221	K562	blood:	n/a	n/a
8	CEBPB	chr12:39350101-39350459	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr12:39392806-39393337	ECC-1	luminal epithelium:	n/a	n/a
10	CEBPB	chr12:39343172-39343523	Hela-S3	cervix:	n/a	chr12:39343343-39343354 chr12:39343343-39343356 chr12:39343344-39343355
11	CEBPB	chr12:39343240-39343484	A549	lung:	n/a	chr12:39343343-39343354 chr12:39343343-39343356 chr12:39343344-39343355
12	CEBPB	chr12:39343218-39343485	HepG2	liver:	n/a	chr12:39343343-39343354 chr12:39343343-39343356 chr12:39343344-39343355
13	CEBPB	chr12:39411626-39411950	K562	blood:	n/a	chr12:39411779-39411790 chr12:39411777-39411788 chr12:39411779-39411788
14	CEBPB	chr12:39411614-39411926	IMR90	lung:	n/a	chr12:39411779-39411790 chr12:39411777-39411788 chr12:39411779-39411788
15	CEBPB	chr12:39408214-39408240	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr12:39348442-39348533	HepG2	liver:	n/a	chr12:39348505-39348514 chr12:39348503-39348516 chr12:39348504-39348515 chr12:39348493-39348504
17	CEBPB	chr12:39371013-39371289	A549	lung:	n/a	n/a
18	CEBPB	chr12:39377482-39377784	HepG2	liver:	n/a	n/a
19	CEBPB	chr12:39318093-39318342	K562	blood:	n/a	n/a
20	CEBPB	chr12:39320075-39320275	HepG2	liver:	n/a	chr12:39320191-39320202 chr12:39320190-39320201
21	CEBPB	chr12:39348440-39348640	A549	lung:	n/a	chr12:39348505-39348514 chr12:39348503-39348516 chr12:39348504-39348515 chr12:39348493-39348504
22	CEBPB	chr12:39343250-39343450	H1-hESC	embryonic stem cell:	n/a	chr12:39343343-39343354 chr12:39343343-39343356 chr12:39343344-39343355
23	CEBPB	chr12:39372998-39373086	HepG2	liver:	n/a	chr12:39373009-39373020
24	CEBPB	chr12:39411637-39411851	HepG2	liver:	n/a	chr12:39411779-39411790 chr12:39411777-39411788 chr12:39411779-39411788
25	CEBPB	chr12:39350020-39350755	ECC-1	luminal epithelium:	n/a	chr12:39350684-39350697
26	CEBPB	chr12:39343143-39343473	ECC-1	luminal epithelium:	n/a	chr12:39343343-39343354 chr12:39343343-39343356 chr12:39343344-39343355
27	CEBPB	chr12:39350056-39350627	ECC-1	luminal epithelium:	n/a	n/a
28	CEBPB	chr12:39372909-39372945	K562	blood:	n/a	n/a
29	CEBPB	chr12:39370988-39371230	HepG2	liver:	n/a	n/a
30	CEBPB	chr12:39376831-39377259	HepG2	liver:	n/a	n/a
31	CEBPD	chr12:39327970-39328180	K562	blood:	n/a	n/a
32	CEBPD	chr12:39327870-39328350	K562	blood:	n/a	n/a
33	CHD1	chr12:39393120-39393166	GM12878	blood:	n/a	n/a
34	CTCF	chr12:39314980-39315130	GM12871	blood:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
35	CTCF	chr12:39314960-39315110	NHLF	lung:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
36	CTCF	chr12:39314723-39315358	SK-N-SH	brain:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
37	CTCF	chr12:39314867-39315326	MCF-7	breast:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
38	CTCF	chr12:39314980-39315130	HRPEpiC	eye:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
39	CTCF	chr12:39397720-39397870	HEEpiC	esophagus:	n/a	n/a
40	CTCF	chr12:39314980-39315130	GM12873	blood:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
41	CTCF	chr12:39314940-39315090	GM12865	blood:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
42	CTCF	chr12:39314980-39315130	HUVEC	blood vessel:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
43	CTCF	chr12:39314980-39315130	HCPEpiC	choroid plexus:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
44	CTCF	chr12:39314949-39315182	NHEK	skin:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
45	CTCF	chr12:39315000-39315150	HPAF	blood vessel:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
46	CTCF	chr12:39397728-39397850	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr12:39314819-39315384	HCT-116	colon:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
48	CTCF	chr12:39314972-39315145	GM20000	blood:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
49	CTCF	chr12:39315020-39315170	AoAF	blood vessel:	n/a	chr12:39315059-39315077 chr12:39315061-39315082 chr12:39315060-39315076 chr12:39315062-39315070 chr12:39315062-39315075
50	CTCF	chr12:39327940-39328090	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:39343718..39345753-chr12:39348375..39350244,2	K562	blood:
2	chr12:39343718..39345753-chr12:39348375..39350244,2	K562	blood:
3	chr12:39314389..39315587-chr12:39497082..39498251,11	MCF-7	breast:
4	chr12:39396332..39398967-chr12:39400620..39403550,2	K562	blood:
5	chr12:39396332..39398967-chr12:39400620..39403550,2	K562	blood:
6	chr12:39315885..39316656-chr16:75018113..75018792,2	MCF-7	breast:
7	chr12:39319182..39321686-chr4:39639319..39641692,2	MCF-7	breast:
8	chr12:39320556..39323665-chr12:39326717..39328717,3	K562	blood:
9	chr12:39295565..39299427-chr12:39307532..39310185,3	K562	blood:
10	chr12:39342874..39345523-chr12:39354497..39356508,3	K562	blood:
11	chr12:39378140..39380661-chr12:39381373..39384205,2	MCF-7	breast:
12	chr12:39342874..39345523-chr12:39354497..39356508,3	K562	blood:
13	chr12:39406167..39408502-chr12:39412272..39414594,2	K562	blood:
14	chr12:39314606..39315315-chr12:39497081..39498041,2	K562	blood:
15	chr12:39314380..39315501-chr12:39497292..39498019,4	MCF-7	breast:
16	chr12:39320556..39323665-chr12:39326717..39328717,3	K562	blood:
17	chr12:39406167..39408502-chr12:39412272..39414594,2	K562	blood:
18	chr12:39378140..39380661-chr12:39381373..39384205,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALG10B-2	chr12:39313439-39313539	XLOC_009709
2	lnc-ALG10B-2	chr12:39317620-39317740	XLOC_009709
3	lnc-CPNE8-3	chr12:39388605-39388738	NONHSAT027694
4	lnc-CPNE8-3	chr12:39390514-39390684	NONHSAT027694

Variant related genes	Relation type
ENSG00000252801	TF binding region
ENSG00000257586	TF binding region
ENSG00000163683	chromatin interactions
ENSG00000255458	chromatin interactions
ENSG00000103091	chromatin interactions

Extended variants
information (count: 1096 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:1096 , 50 per page) page: 1 2 3 4 5 6 7 ... 22

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1878224	chr12:39309714-39309715	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs368693420	chr12:39309753-39309754	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs556397741	chr12:39309790-39309791	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs373785362	chr12:39309793-39309794	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs200713516	chr12:39309888-39309889	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs374426679	chr12:39309979-39309980	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs545184720	chr12:39310098-39310099	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs11831499	chr12:39310114-39310115	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs11831502	chr12:39310127-39310128	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs540641364	chr12:39310158-39310159	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs534533877	chr12:39310164-39310165	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs560517381	chr12:39310207-39310208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs567267116	chr12:39310238-39310239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs151147357	chr12:39310295-39310296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs563185652	chr12:39310304-39310305	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs140213303	chr12:39310319-39310320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs551930660	chr12:39310327-39310328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs78434957	chr12:39310340-39310341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs571686858	chr12:39310342-39310343	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs372006069	chr12:39310351-39310352	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs527753805	chr12:39310393-39310394	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs143904525	chr12:39310487-39310488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs373602653	chr12:39310511-39310512	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs536561563	chr12:39310538-39310539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs556225663	chr12:39310549-39310550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs180851632	chr12:39310556-39310557	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs7968397	chr12:39310591-39310592	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs549743879	chr12:39310596-39310597	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs571285349	chr12:39310616-39310617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs535204283	chr12:39310637-39310638	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs146054992	chr12:39310644-39310645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs7971601	chr12:39310651-39310652	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs186491742	chr12:39310665-39310666	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs7974510	chr12:39310730-39310731	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs574133569	chr12:39310770-39310771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs543013538	chr12:39310775-39310776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs7957071	chr12:39310799-39310800	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs532020209	chr12:39310830-39310831	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs545290604	chr12:39310834-39310835	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs146877792	chr12:39310883-39310884	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs527790692	chr12:39310890-39310891	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs11169983	chr12:39310913-39310914	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs140681616	chr12:39310940-39310941	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs35134389	chr12:39310981-39310982	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs550131807	chr12:39311002-39311003	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs546357367	chr12:39311023-39311024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs555298189	chr12:39311035-39311036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs576838887	chr12:39311041-39311042	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs34476057	chr12:39311083-39311084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs538896523	chr12:39311139-39311140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

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
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	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
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39308800-39310000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:39309200-39309800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:39310000-39313000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:39311800-39312400	Enhancers	HMEC	breast
5	chr12:39311800-39312600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:39311800-39313000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39311800-39313200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:39311800-39313800	Enhancers	NHEK	skin
9	chr12:39313000-39313600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:39316400-39317000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr12:39324800-39325000	ZNF genes & repeats	K562	blood
12	chr12:39325000-39327400	Weak transcription	K562	blood
13	chr12:39325200-39325800	Enhancers	HepG2	liver
14	chr12:39327400-39328000	Enhancers	K562	blood
15	chr12:39347800-39348400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr12:39347800-39348600	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr12:39348000-39348600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:39348600-39349200	Enhancers	Fetal Brain Male	brain
19	chr12:39349600-39351000	Enhancers	Hela-S3	cervix
20	chr12:39350000-39350400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:39350000-39350800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:39350400-39350800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:39350400-39350800	Enhancers	NH-A	brain
24	chr12:39354400-39356600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr12:39355000-39356800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr12:39355000-39356800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:39355200-39356400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr12:39355400-39356400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:39355400-39356600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr12:39355400-39356600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:39363000-39363600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:39363000-39364400	Enhancers	Fetal Brain Male	brain
33	chr12:39375200-39375400	ZNF genes & repeats	Pancreas	Pancrea
34	chr12:39376400-39376600	Enhancers	HepG2	liver
35	chr12:39376400-39377000	Active TSS	A549	lung
36	chr12:39376600-39377200	Active TSS	HepG2	liver
37	chr12:39376800-39377200	Active TSS	Osteobl	bone
38	chr12:39377000-39377200	Flanking Active TSS	A549	lung
39	chr12:39377200-39377800	Flanking Active TSS	HepG2	liver
40	chr12:39388800-39389200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr12:39389000-39389400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:39396200-39396400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:39396200-39396400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:39396400-39396800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:39396400-39397400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:39396800-39397800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr12:39396800-39399400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:39397400-39397800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:39404200-39405800	Enhancers	Brain Germinal Matrix	brain

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