Variant report

Variant	esv3388226
Chromosome Location	chr4:88267578-88275176
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	BCLAF1	chr4:88274531-88275047	GM12878	blood:	n/a	n/a
2	BRCA1	chr4:88274711-88274757	GM12878	blood:	n/a	n/a
3	BRCA1	chr4:88274849-88275046	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr4:88274648-88274960	HepG2	liver:	n/a	n/a
5	CEBPB	chr4:88274583-88274924	MCF-7	breast:	n/a	n/a
6	CEBPB	chr4:88274654-88274987	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr4:88274621-88275554	IMR90	lung:	n/a	chr4:88275098-88275111
8	CEBPB	chr4:88274643-88274980	A549	lung:	n/a	n/a
9	CEBPB	chr4:88274649-88274999	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr4:88274671-88274892	K562	blood:	n/a	n/a
11	CHD2	chr4:88274687-88274868	K562	blood:	n/a	n/a
12	CTCF	chr4:88274729-88274902	A549	lung:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
13	CTCF	chr4:88274702-88274939	SK-N-SH_RA	brain:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
14	CTCF	chr4:88274780-88274930	HCM	heart:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
15	CTCF	chr4:88274740-88274890	GM12867	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
16	CTCF	chr4:88274760-88274910	GM12872	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
17	CTCF	chr4:88274760-88274910	SAEC	small airway:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
18	CTCF	chr4:88274720-88274870	AG09309	skin:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
19	CTCF	chr4:88274712-88274950	Hela-S3	cervix:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
20	CTCF	chr4:88274717-88274939	T-47D	breast:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
21	CTCF	chr4:88274708-88274951	GM10248	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
22	CTCF	chr4:88274780-88274930	Caco-2	colon:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
23	CTCF	chr4:88274730-88274954	GM12892	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
24	CTCF	chr4:88274760-88274910	AG10803	skin:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
25	CTCF	chr4:88274760-88274910	HMEC	breast:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
26	CTCF	chr4:88274718-88274949	Fibrobl	skin:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
27	CTCF	chr4:88274780-88274930	HUVEC	blood vessel:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
28	CTCF	chr4:88274680-88274830	HCT-116	colon:	n/a	n/a
29	CTCF	chr4:88274720-88274870	GM12874	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
30	CTCF	chr4:88274700-88274850	HRE	kidney:	n/a	chr4:88274829-88274847 chr4:88274830-88274846
31	CTCF	chr4:88274688-88274964	HUVEC	blood vessel:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
32	CTCF	chr4:88274780-88274930	MCF-7	breast:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
33	CTCF	chr4:88274760-88274910	AoAF	blood vessel:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
34	CTCF	chr4:88274698-88274971	ECC-1	luminal epithelium:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
35	CTCF	chr4:88274740-88274890	SK-N-SH_RA	brain:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
36	CTCF	chr4:88274508-88275154	SK-N-SH	brain:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
37	CTCF	chr4:88274780-88274930	GM12870	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
38	CTCF	chr4:88274693-88274986	K562	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
39	CTCF	chr4:88274740-88274890	HA-sp	spinal cord:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
40	CTCF	chr4:88274760-88274910	GM12869	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
41	CTCF	chr4:88274720-88274870	NHLF	lung:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
42	CTCF	chr4:88274740-88274890	GM12865	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
43	CTCF	chr4:88274720-88274870	A549	lung:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
44	CTCF	chr4:88274652-88275039	IMR90	lung:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
45	CTCF	chr4:88274728-88274964	GM19240	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
46	CTCF	chr4:88274760-88274910	HMF	breast:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
47	CTCF	chr4:88274703-88274943	GM10266	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
48	CTCF	chr4:88274740-88274890	RPTEC	kidney:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
49	CTCF	chr4:88274622-88275050	GM12878	blood:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846
50	CTCF	chr4:88274800-88274950	HFF-Myc	foreskin:	n/a	chr4:88274829-88274847 chr4:88274831-88274852 chr4:88274830-88274846

No.	Distal block	Cell Line	Cell type
1	chr4:88274390..88275203-chr4:88387077..88388072,3	K562	blood:
2	chr4:88274380..88275024-chr4:88386955..88387766,2	MCF-7	breast:
3	chr4:88274412..88275303-chr4:88464991..88465582,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NUDT9-1	chr4:88273499-88273744	expReg_chr4_4651_+

Variant related genes	Relation type
ENSG00000255723	TF binding region

Extended variants
information (count: 187 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:187 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534915900	chr4:88267611-88267612	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs187782701	chr4:88267618-88267619	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs183315514	chr4:88267644-88267645	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs56788263	chr4:88267672-88267673	ZNF genes & repeats Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs543011222	chr4:88267716-88267717	ZNF genes & repeats Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs559989258	chr4:88267717-88267718	ZNF genes & repeats Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs576584272	chr4:88267740-88267741	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs544064829	chr4:88267741-88267742	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs371246064	chr4:88267780-88267781	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs565468359	chr4:88267781-88267782	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs532739711	chr4:88267812-88267813	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs569678703	chr4:88267829-88267830	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs559755372	chr4:88267842-88267843	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs9991773	chr4:88267875-88267876	ZNF genes & repeats Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs79888167	chr4:88267947-88267948	ZNF genes & repeats Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs139032642	chr4:88267977-88267978	ZNF genes & repeats Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs149888841	chr4:88267994-88267995	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs190504087	chr4:88267997-88267998	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs115516242	chr4:88268035-88268036	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs183035098	chr4:88268039-88268040	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs187752463	chr4:88268046-88268047	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs192628300	chr4:88268053-88268054	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs142404354	chr4:88268080-88268081	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs75347655	chr4:88268084-88268085	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs528066988	chr4:88268202-88268203	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs184294687	chr4:88268211-88268212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs554987506	chr4:88268221-88268222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs373127384	chr4:88268256-88268257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs55882062	chr4:88268267-88268268	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs13105267	chr4:88268268-88268269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs202008928	chr4:88268269-88268270	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs56808195	chr4:88268270-88268271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs13132871	chr4:88268271-88268272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs576651228	chr4:88268282-88268283	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs70957224	chr4:88268288-88268289	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs13105100	chr4:88268289-88268290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs7689292	chr4:88268341-88268342	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs367940270	chr4:88268383-88268384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs558733617	chr4:88268432-88268433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs113304502	chr4:88268789-88268790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs113023408	chr4:88268803-88268804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs201211511	chr4:88268920-88268921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs202140208	chr4:88269354-88269355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs200374579	chr4:88269595-88269596	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs577377007	chr4:88269996-88269997	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs372126964	chr4:88270051-88270052	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs201193178	chr4:88270087-88270088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs374272898	chr4:88270178-88270179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs368382375	chr4:88271927-88271928	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs541232052	chr4:88272056-88272057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Olfactory neuroblastoma	18408657	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
Acute monocytic leukemia	16498392	CNVD
Multiple myeloma	16616336	CNVD
Esophageal adenocarcinoma	18820669	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	22522925	CNVD
Myelofibrosis	22110671	CNVD
Parkinson disease	20877625	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:200 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88253800-88274600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:88255000-88268200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:88255200-88267800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr4:88255200-88274400	Weak transcription	GM12878-XiMat	blood
7	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:88256000-88274800	Weak transcription	A549	lung
11	chr4:88256200-88292800	Weak transcription	Gastric	stomach
12	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
13	chr4:88257000-88291000	Weak transcription	HUVEC	blood vessel
14	chr4:88257600-88267600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:88258000-88278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:88258000-88285400	Weak transcription	Small Intestine	intestine
18	chr4:88259200-88277200	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:88259200-88283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:88261000-88280000	Weak transcription	Left Ventricle	heart
21	chr4:88261000-88283200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:88261200-88285000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:88262200-88280200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:88262600-88274200	Weak transcription	K562	blood
25	chr4:88262600-88274400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:88262800-88267600	Weak transcription	Ovary	ovary
27	chr4:88263000-88267600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:88263000-88267600	Weak transcription	Placenta	Placenta
29	chr4:88263000-88274600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:88263000-88274600	Weak transcription	Colonic Mucosa	Colon
31	chr4:88263000-88277000	Weak transcription	Lung	lung
32	chr4:88263000-88277000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:88263000-88278000	Weak transcription	Stomach Mucosa	stomach
34	chr4:88263000-88280000	Weak transcription	Pancreas	Pancrea
35	chr4:88263200-88281600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:88263600-88274600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:88264000-88277000	Weak transcription	HSMM	muscle
38	chr4:88264200-88285600	Weak transcription	Spleen	Spleen
39	chr4:88264400-88279800	Weak transcription	Hela-S3	cervix
40	chr4:88265400-88267800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:88265400-88267800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr4:88265600-88267600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:88265600-88267600	Strong transcription	HepG2	liver
44	chr4:88265600-88267800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr4:88265600-88268000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr4:88265600-88268000	Strong transcription	Fetal Thymus	thymus
47	chr4:88265800-88268000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:88265800-88268000	Strong transcription	Liver	Liver
49	chr4:88265800-88268200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:88266000-88267600	ZNF genes & repeats	Primary B cells from cord blood	blood

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