Variant report

Variant	esv16085
Chromosome Location	chr12:50355200-50355978
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:50355870-50355957	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr12:50355020-50355563	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr12:50355662-50356123	H1-hESC	embryonic stem cell:	n/a	chr12:50355673-50355688
4	E2F6	chr12:50355084-50355660	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr12:50355702-50355945	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr12:50355136-50355444	H1-hESC	embryonic stem cell:	n/a	n/a
7	GTF2F1	chr12:50355350-50355360	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:50355069-50355604	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr12:50355683-50356169	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr12:50355155-50355579	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr12:50355245-50355513	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr12:50355794-50356111	H1-hESC	embryonic stem cell:	n/a	n/a
13	MXI1	chr12:50355772-50355855	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:50355889-50355921	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr12:50355665-50356084	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr12:50355897-50355999	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3A	chr12:50355845-50355954	H1-hESC	embryonic stem cell:	n/a	n/a
18	SUZ12	chr12:50354404-50355991	NT2-D1	testis:	n/a	n/a
19	TBP	chr12:50355749-50355932	H1-hESC	embryonic stem cell:	n/a	n/a
20	TBP	chr12:50355362-50355369	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF1	chr12:50355218-50355566	SK-N-SH_RA	brain:	n/a	chr12:50355512-50355528
22	USF1	chr12:50355192-50355505	H1-hESC	embryonic stem cell:	n/a	n/a
23	USF1	chr12:50355340-50355496	GM12878	blood:	n/a	n/a
24	USF1	chr12:50355141-50355572	H1-hESC	embryonic stem cell:	n/a	chr12:50355512-50355528
25	USF1	chr12:50355245-50355492	SK-N-SH_RA	brain:	n/a	n/a
26	USF2	chr12:50355868-50356048	H1-hESC	embryonic stem cell:	n/a	n/a
27	USF2	chr12:50355246-50355581	H1-hESC	embryonic stem cell:	n/a	chr12:50355512-50355528
28	YY1	chr12:50355939-50356132	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZBTB7A	chr12:50355912-50357521	ECC-1	luminal epithelium:	n/a	n/a
30	ZNF143	chr12:50355745-50355990	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZNF143	chr12:50355353-50355509	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:50355821-50355871	BE2_C	brain:	n/a
2	chr12:50355821-50355871	NT2-D1	testis:	n/a
3	chr12:50355821-50355871	HAEpiC	amniotic membrane:	n/a
4	chr12:50355307-50355357	HCT-116	colon:	n/a
5	chr12:50355821-50355871	NB4	blood:	n/a
6	chr12:50355307-50355357	MCF-7	breast:	n/a
7	chr12:50355821-50355871	AG04449	skin:	fetal
8	chr12:50355307-50355357	GM12892	blood:	n/a
9	chr12:50355821-50355871	GM12878	blood:	n/a
10	chr12:50355307-50355357	PFSK-1	brain:	n/a
11	chr12:50355821-50355871	HUVEC	blood vessel:	n/a
12	chr12:50355821-50355871	A549	lung:	n/a
13	chr12:50355821-50355871	PFSK-1	brain:	n/a
14	chr12:50355821-50355871	HL-60	blood:	n/a
15	chr12:50355307-50355357	HepG2	liver:	n/a
16	chr12:50355821-50355871	ovcar-3	ovarian:	n/a
17	chr12:50355821-50355871	Caco-2	colon:	n/a
18	chr12:50355307-50355357	H1-hESC	embryonic stem cell:	embryo
19	chr12:50355821-50355871	AG09319	gingival:	n/a
20	chr12:50355307-50355357	GM12891	blood:	n/a
21	chr12:50355821-50355871	HCPEpiC	choroid plexus:	n/a
22	chr12:50355307-50355357	Hepatocyte	liver:	n/a
23	chr12:50355307-50355357	HCPEpiC	choroid plexus:	n/a
24	chr12:50355821-50355871	SK-N-MC	brain:	n/a
25	chr12:50355307-50355357	SK-N-SH_RA	brain:	n/a
26	chr12:50355821-50355871	PANC-1	pancreas:	n/a
27	chr12:50355821-50355871	BJ	skin:	n/a
28	chr12:50355307-50355357	HCM	heart:	n/a
29	chr12:50355307-50355357	SK-N-MC	brain:	n/a
30	chr12:50355307-50355357	BJ	skin:	n/a
31	chr12:50355307-50355357	NHDF-neo	bronchial:	n/a
32	chr12:50355821-50355871	HRCEpiC	kidney:	n/a
33	chr12:50355821-50355871	AG09309	skin:	n/a
34	chr12:50355307-50355357	GM19239	blood:	n/a
35	chr12:50355307-50355357	SKMC	muscle:	n/a
36	chr12:50355307-50355357	T-47D	breast:	n/a
37	chr12:50355307-50355357	HPAEpiC	pulmonary alveolar:	n/a
38	chr12:50355821-50355871	GM12892	blood:	n/a
39	chr12:50355821-50355871	GM12891	blood:	n/a
40	chr12:50355821-50355871	NHBE	bronchial:	n/a
41	chr12:50355821-50355871	HNPCEpiC	eye:	n/a
42	chr12:50355821-50355871	NH-A	brain:	n/a
43	chr12:50355821-50355871	IMR90	lung:	fetal
44	chr12:50355307-50355357	RPTEC	kidney:	n/a
45	chr12:50355307-50355357	HRPEpiC	eye:	n/a
46	chr12:50355307-50355357	GM06990	blood:	n/a
47	chr12:50355821-50355871	SK-N-SH_RA	brain:	n/a
48	chr12:50355821-50355871	NHDF-neo	bronchial:	n/a
49	chr12:50355307-50355357	HEK293	kidney:	embryo
50	chr12:50355307-50355357	SK-N-SH	brain:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50353765..50356841-chr12:50356981..50360242,4	MCF-7	breast:

No data

Variant related genes	Relation type
AQP5	TF binding region
AQP6	TF binding region
AQP5	CpG island
AQP6	CpG island
ENSG00000161798	chromatin interactions

Extended variants
information (count: 21 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534093655	chr12:50355200-50355201	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs547054919	chr12:50355274-50355275	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs145951089	chr12:50355316-50355317	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs185659043	chr12:50355354-50355355	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs559114758	chr12:50355432-50355433	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs569298532	chr12:50355789-50355790	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs538064477	chr12:50355791-50355792	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs555099046	chr12:50355812-50355813	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs575071552	chr12:50355832-50355833	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs532533853	chr12:50355846-50355847	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs138665659	chr12:50355847-50355848	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs540509756	chr12:50355854-50355855	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs568521335	chr12:50355864-50355865	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs142676062	chr12:50355871-50355872	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs139623970	chr12:50355888-50355889	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs143334982	chr12:50355899-50355900	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs146740002	chr12:50355906-50355907	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs398123054	chr12:50355913-50355914	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs398123055	chr12:50355934-50355935	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs199524477	chr12:50355937-50355938	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs139174720	chr12:50355954-50355955	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

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
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
Cancer	17160897	CNVD
Melanoma	20877625	CNVD
Cancer	20164919	CNVD

Chromatin state (count:167 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50352800-50355400	Enhancers	Lung	lung
2	chr12:50353000-50357400	Enhancers	HMEC	breast
3	chr12:50353200-50355200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:50353200-50355200	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr12:50353200-50355200	Enhancers	Gastric	stomach
6	chr12:50353400-50355200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
7	chr12:50353400-50355200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr12:50353400-50355200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr12:50353400-50355200	Bivalent Enhancer	NH-A	brain
10	chr12:50353400-50355400	Bivalent Enhancer	Fetal Lung	lung
11	chr12:50353400-50357400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:50353600-50357200	Bivalent Enhancer	Fetal Intestine Small	intestine
13	chr12:50353600-50358400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:50354000-50355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:50354000-50356200	Bivalent Enhancer	Spleen	Spleen
16	chr12:50354200-50355200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
17	chr12:50354400-50355200	Bivalent Enhancer	Stomach Mucosa	stomach
18	chr12:50354400-50355800	Bivalent Enhancer	Small Intestine	intestine
19	chr12:50354600-50355200	Bivalent Enhancer	Placenta	Placenta
20	chr12:50354600-50355200	Weak transcription	HSMM	muscle
21	chr12:50354600-50355200	Bivalent/Poised TSS	NHEK	skin
22	chr12:50354600-50355400	Bivalent Enhancer	Primary B cells from cord blood	blood
23	chr12:50354600-50355400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr12:50354600-50355400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr12:50354600-50355400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:50354600-50355400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:50354600-50355400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
28	chr12:50354600-50355800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:50354600-50356000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr12:50354600-50356400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:50354800-50355200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
32	chr12:50354800-50355200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:50354800-50355200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:50354800-50355200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:50354800-50355200	Enhancers	Liver	Liver
36	chr12:50354800-50355200	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr12:50354800-50355200	Bivalent/Poised TSS	Fetal Brain Female	brain
38	chr12:50354800-50355200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
39	chr12:50354800-50355200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
40	chr12:50354800-50355400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
41	chr12:50354800-50355400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr12:50354800-50355400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:50354800-50355400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:50354800-50355400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:50354800-50355400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr12:50354800-50355400	Bivalent Enhancer	Fetal Brain Male	brain
47	chr12:50354800-50355400	Enhancers	Fetal Heart	heart
48	chr12:50354800-50355400	Flanking Active TSS	Right Ventricle	heart
49	chr12:50354800-50355600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:50354800-50355600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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