Variant report

Variant	esv275364
Chromosome Location	chr2:55621732-55632233
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	chr2:55623002-55623354	GM12878	blood:	n/a	n/a
2	BHLHE40	chr2:55622905-55623263	GM12878	blood:	n/a	n/a
3	CEBPB	chr2:55630386-55630675	HepG2	liver:	n/a	chr2:55630545-55630556
4	CEBPB	chr2:55630444-55630590	K562	blood:	n/a	chr2:55630545-55630556
5	CEBPB	chr2:55626610-55626692	K562	blood:	n/a	n/a
6	CEBPB	chr2:55622448-55622479	HepG2	liver:	n/a	n/a
7	EP300	chr2:55627212-55628297	SK-N-SH	brain:	n/a	chr2:55628118-55628128 chr2:55627733-55627747
8	EP300	chr2:55627439-55627698	SK-N-SH_RA	brain:	n/a	n/a
9	EP300	chr2:55627469-55627717	SK-N-SH_RA	brain:	n/a	n/a
10	FOS	chr2:55624017-55624327	HUVEC	blood vessel:	n/a	chr2:55624146-55624155 chr2:55624120-55624131
11	FOS	chr2:55627167-55627227	MCF10A-Er-Src	breast:	n/a	n/a
12	FOSL2	chr2:55626950-55627504	SK-N-SH	brain:	n/a	n/a
13	GATA2	chr2:55627807-55628000	SH-SY5Y	brain:	n/a	chr2:55627848-55627855
14	GATA3	chr2:55627273-55628179	SK-N-SH	brain:	n/a	chr2:55627848-55627855
15	GATA3	chr2:55626181-55626357	SH-SY5Y	brain:	n/a	n/a
16	GATA3	chr2:55627702-55628150	SH-SY5Y	brain:	n/a	chr2:55627848-55627855
17	JUN	chr2:55622530-55622583	HepG2	liver:	n/a	n/a
18	JUND	chr2:55622393-55622594	HepG2	liver:	n/a	n/a
19	MAFF	chr2:55630533-55630781	HepG2	liver:	n/a	chr2:55630666-55630684
20	MAFK	chr2:55631296-55631460	HepG2	liver:	n/a	n/a
21	MAFK	chr2:55630653-55630728	IMR90	lung:	n/a	n/a
22	MAFK	chr2:55630552-55630803	HepG2	liver:	n/a	n/a
23	MEF2A	chr2:55623057-55623354	GM12878	blood:	n/a	chr2:55623226-55623243
24	NFIC	chr2:55622901-55623459	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:55625809-55625844	ProgFib	skin:	n/a	n/a
26	POLR2A	chr2:55627795-55628087	K562	blood:	n/a	n/a
27	POLR2A	chr2:55632175-55632531	K562	blood:	n/a	n/a
28	RFX5	chr2:55626114-55626221	K562	blood:	n/a	n/a
29	RUNX3	chr2:55622941-55623684	GM12878	blood:	n/a	n/a
30	TCF12	chr2:55629287-55629763	SK-N-SH	brain:	n/a	n/a
31	TCF12	chr2:55627351-55628125	SK-N-SH	brain:	n/a	n/a
32	USF2	chr2:55623002-55623250	GM12878	blood:	n/a	n/a
33	YY1	chr2:55627382-55627708	SK-N-SH_RA	brain:	n/a	chr2:55627590-55627598
34	ZNF384	chr2:55623032-55623249	GM12878	blood:	n/a	n/a
35	ZNF384	chr2:55628449-55628525	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55627632..55629326-chr2:55632488..55634437,2	K562	blood:
2	chr2:55627338..55628874-chr2:55629453..55631312,2	MCF-7	breast:
3	chr2:55627338..55628874-chr2:55629453..55631312,2	MCF-7	breast:
4	chr2:55629189..55632200-chr2:55632234..55637417,4	K562	blood:
5	chr2:55615003..55618126-chr2:55622970..55626824,3	K562	blood:
6	chr2:55618745..55621738-chr2:55622062..55625126,3	K562	blood:
7	chr2:55618745..55621738-chr2:55622062..55625126,3	K562	blood:
8	chr2:55624788..55628704-chr2:55629085..55632054,3	K562	blood:
9	chr2:55629328..55632200-chr2:55634808..55637417,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTIF2-4	chr2:55628085-55628362	expReg_chr2_4282_-

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000115355	chromatin interactions

Extended variants
information (count: 466 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:466 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs149305491	chr2:55621732-55621733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs543736253	chr2:55621774-55621775	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs556964875	chr2:55621800-55621801	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs548173526	chr2:55621841-55621842	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs576754881	chr2:55621884-55621885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs545894080	chr2:55621908-55621909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs565959257	chr2:55621920-55621921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs186571611	chr2:55621939-55621940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs200597290	chr2:55621951-55621952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs77195988	chr2:55621958-55621959	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs199764992	chr2:55621962-55621963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs568036369	chr2:55621985-55621986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs574473855	chr2:55621990-55621991	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs192633548	chr2:55621996-55621997	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs375064762	chr2:55622035-55622036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs7570934	chr2:55622046-55622047	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs561532750	chr2:55622047-55622048	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs530878754	chr2:55622059-55622060	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs550588357	chr2:55622066-55622067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs4535081	chr2:55622074-55622075	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs532354202	chr2:55622130-55622131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs570736405	chr2:55622131-55622132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs539738627	chr2:55622137-55622138	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs145422502	chr2:55622149-55622150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs553290757	chr2:55622162-55622163	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs555230430	chr2:55622166-55622167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs573489084	chr2:55622167-55622168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs184103416	chr2:55622173-55622174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs377278845	chr2:55622189-55622190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs147247028	chr2:55622260-55622261	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs576777138	chr2:55622261-55622262	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs545455760	chr2:55622289-55622290	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs552669216	chr2:55622314-55622315	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs567203494	chr2:55622328-55622329	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs555753300	chr2:55622356-55622357	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs370061974	chr2:55622384-55622385	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs5831362	chr2:55622392-55622393	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs2867174	chr2:55622431-55622432	Enhancers Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
39	rs541518811	chr2:55622462-55622463	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs544751232	chr2:55622486-55622487	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs561584964	chr2:55622494-55622495	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs115547180	chr2:55622511-55622512	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188657854	chr2:55622531-55622532	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs2867175	chr2:55622549-55622550	Enhancers Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs148707139	chr2:55622566-55622567	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs1902056	chr2:55622624-55622625	Enhancers Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs75311999	chr2:55622625-55622626	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs2867176	chr2:55622685-55622686	Enhancers Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs151337398	chr2:55622689-55622690	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs553512317	chr2:55622697-55622698	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ependymoma	20639864	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:249 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
4	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
6	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
9	chr2:55589600-55628800	Weak transcription	Fetal Thymus	thymus
10	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:55590400-55622400	Weak transcription	GM12878-XiMat	blood
12	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:55592800-55626600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
17	chr2:55593000-55622400	Weak transcription	Brain Angular Gyrus	brain
18	chr2:55593000-55622400	Weak transcription	Brain Anterior Caudate	brain
19	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:55599200-55626800	Weak transcription	Osteobl	bone
22	chr2:55600600-55631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:55600800-55629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:55600800-55629400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:55602000-55629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:55602200-55629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:55602400-55629600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:55603600-55629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:55603600-55630200	Weak transcription	NH-A	brain
32	chr2:55606200-55630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:55608600-55630400	Weak transcription	HSMM	muscle
34	chr2:55612600-55629600	Weak transcription	Dnd41	blood
35	chr2:55612600-55630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
37	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
38	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:55616600-55635400	Weak transcription	HMEC	breast
40	chr2:55616800-55622400	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:55616800-55630200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
43	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
44	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
45	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
47	chr2:55618400-55622400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr2:55618400-55627000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr2:55618600-55622800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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