Variant report

Variant	esv3458776
Chromosome Location	chr2:179308111-179309151
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:179308354-179308460	K562	blood:	n/a	n/a
2	CTCF	chr2:179308200-179308350	GM12873	blood:	n/a	n/a
3	CTCF	chr2:179308780-179308930	Caco-2	colon:	n/a	n/a
4	CTCF	chr2:179308300-179308450	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr2:179308337-179308488	MCF-7	breast:	n/a	n/a
6	CTCF	chr2:179308326-179308484	MCF-7	breast:	n/a	n/a
7	CTCF	chr2:179308320-179308470	HBMEC	blood vessel:	n/a	n/a
8	CTCF	chr2:179308320-179308470	Caco-2	colon:	n/a	n/a
9	CTCF	chr2:179308320-179308470	K562	blood:	n/a	n/a
10	CTCF	chr2:179308300-179308450	MCF-7	breast:	n/a	n/a
11	CTCF	chr2:179308362-179308435	HepG2	liver:	n/a	n/a
12	CTCF	chr2:179308360-179308510	HepG2	liver:	n/a	n/a
13	CTCF	chr2:179308340-179308490	A549	lung:	n/a	n/a
14	CTCF	chr2:179308360-179308510	AG04449	skin:	n/a	n/a
15	CTCF	chr2:179308308-179308469	HepG2	liver:	n/a	n/a
16	CTCF	chr2:179308375-179308437	GM12878	blood:	n/a	n/a
17	JUN	chr2:179309133-179309186	K562	blood:	n/a	n/a
18	MAX	chr2:179308556-179308667	NB4	blood:	n/a	n/a
19	NFYB	chr2:179309048-179309298	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:179308366-179308918	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:179309033-179309077	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:179309004-179309008	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:179308609-179308746	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:179308749-179308824	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:179309144-179310551	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:179309113-179309116	GM12878	blood:	n/a	n/a
27	RAD21	chr2:179308325-179308481	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr2:179308280-179308490	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179308416..179311292-chr2:179342166..179344945,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRKRA	TF binding region
ENSG00000079150	chromatin interactions

Extended variants
information (count: 48 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:48 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs148370338	chr2:179308113-179308114	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs200249113	chr2:179308114-179308115	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs75610815	chr2:179308276-179308277	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs79385157	chr2:179308298-179308299	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs543389725	chr2:179308317-179308318	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs111662983	chr2:179308327-179308328	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs547688975	chr2:179308350-179308351	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs528706249	chr2:179308372-179308373	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs540735802	chr2:179308468-179308469	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs564184915	chr2:179308488-179308489	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs2288320	chr2:179308502-179308503	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs549740437	chr2:179308511-179308512	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs569357925	chr2:179308514-179308515	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs529102361	chr2:179308515-179308516	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs2288321	chr2:179308520-179308521	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs565502152	chr2:179308521-179308522	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs534842460	chr2:179308524-179308525	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs148474248	chr2:179308559-179308560	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs74955771	chr2:179308560-179308561	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs571701552	chr2:179308574-179308575	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs569426298	chr2:179308612-179308613	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs538026181	chr2:179308624-179308625	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs537190510	chr2:179308644-179308645	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs192873520	chr2:179308666-179308667	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs199689203	chr2:179308668-179308669	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs62176109	chr2:179308733-179308734	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs552340902	chr2:179308736-179308737	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs574089340	chr2:179308737-179308738	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs536908178	chr2:179308749-179308750	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs553719721	chr2:179308755-179308756	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs145263960	chr2:179308810-179308811	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs545566816	chr2:179308839-179308840	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs184436836	chr2:179308854-179308855	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs377293133	chr2:179308862-179308863	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs577661818	chr2:179308899-179308900	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs11674473	chr2:179308905-179308906	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs543154792	chr2:179308937-179308938	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs562902866	chr2:179308955-179308956	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs115197923	chr2:179308966-179308967	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs548835515	chr2:179308992-179308993	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs571781202	chr2:179309026-179309027	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs559201604	chr2:179309047-179309048	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs548451433	chr2:179309052-179309053	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs551544379	chr2:179309069-179309070	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs368620024	chr2:179309108-179309109	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs563570861	chr2:179309110-179309111	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs201062425	chr2:179309133-179309134	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs202008461	chr2:179309147-179309148	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
Colorectal cancer	16272173	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Glioblastoma	21080181	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Prostate cancer	18632612	CNVD
Sudden cardiac death	19188705	CNVD
Acute myeloid leukemia	20729466	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	18923514	CNVD
Schizophrenia	22241247	CNVD
Mental retardation	21062444	CNVD
Facial dysmorphism	20548289	CNVD
Mental retardation	20548289	CNVD
Schizophrenia	19348701	CNVD
Muscular dystrophy	17160897	CNVD
Cardiomyopathy	17576883	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
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:146 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179279800-179313800	Weak transcription	Stomach Mucosa	stomach
2	chr2:179280000-179310600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:179280200-179314600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:179290200-179312800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:179290800-179312000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:179290800-179312600	Strong transcription	Dnd41	blood
7	chr2:179291000-179311600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:179291000-179313200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:179291000-179313400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:179291000-179313600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:179291200-179310400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr2:179291200-179312200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:179291200-179312800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:179291200-179312800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:179291200-179312800	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:179291200-179313600	Strong transcription	Fetal Thymus	thymus
17	chr2:179291200-179313800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:179291400-179311400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:179291400-179312600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:179291400-179312800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:179291400-179313400	Strong transcription	HSMM	muscle
22	chr2:179291400-179313600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:179291600-179312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:179291600-179312800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:179291600-179312800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:179291600-179313200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:179291600-179313400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:179291600-179313600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:179291800-179313000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:179291800-179314000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:179292000-179314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:179292400-179312800	Weak transcription	Fetal Heart	heart
33	chr2:179293200-179312600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:179293600-179313000	Strong transcription	Liver	Liver
35	chr2:179293800-179310200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:179293800-179313600	Strong transcription	Adipose Nuclei	Adipose
37	chr2:179293800-179313800	Strong transcription	HUVEC	blood vessel
38	chr2:179294000-179313000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:179294200-179314200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:179295400-179311000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:179295400-179311600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:179295400-179312800	Strong transcription	HepG2	liver
43	chr2:179295400-179313600	Strong transcription	Fetal Intestine Large	intestine
44	chr2:179295400-179314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:179297000-179313200	Weak transcription	Right Atrium	heart
46	chr2:179298400-179310200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:179298600-179314400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:179299600-179310000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:179299600-179314800	Weak transcription	Small Intestine	intestine
50	chr2:179299800-179308400	Weak transcription	Colonic Mucosa	Colon

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