Variant report

Variant	nsv10559
Chromosome Location	chr4:122281398-122292297
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	chr4:122291909-122292227	K562	blood:	n/a	n/a
2	CEBPB	chr4:122288309-122288515	HepG2	liver:	n/a	chr4:122288383-122288394
3	CTCF	chr4:122292000-122292150	HRPEpiC	eye:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
4	CTCF	chr4:122291980-122292130	AG04450	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
5	CTCF	chr4:122291960-122292110	HEEpiC	esophagus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
6	CTCF	chr4:122291920-122292070	HAc	cerebellar:	n/a	n/a
7	CTCF	chr4:122292060-122292210	GM12873	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
8	CTCF	chr4:122292020-122292170	AG09309	skin:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
9	CTCF	chr4:122291876-122292196	MCF-7	breast:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
10	CTCF	chr4:122291986-122292129	A549	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
11	CTCF	chr4:122291980-122292130	GM12866	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
12	CTCF	chr4:122291940-122292090	GM12865	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089
13	CTCF	chr4:122291920-122292187	K562	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
14	CTCF	chr4:122291711-122291832	GM19240	blood:	n/a	n/a
15	CTCF	chr4:122291974-122292188	GM10266	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
16	CTCF	chr4:122292020-122292170	GM12872	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
17	CTCF	chr4:122292000-122292150	BJ	skin:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
18	CTCF	chr4:122291887-122292255	K562	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
19	CTCF	chr4:122291985-122292145	SK-N-SH_RA	brain:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
20	CTCF	chr4:122292020-122292170	HCPEpiC	choroid plexus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
21	CTCF	chr4:122291920-122292070	HFF	foreskin:	n/a	n/a
22	CTCF	chr4:122291936-122292227	HUVEC	blood vessel:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
23	CTCF	chr4:122291960-122292110	AoAF	blood vessel:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
24	CTCF	chr4:122291980-122292130	GM12865	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
25	CTCF	chr4:122291900-122292050	HMEC	breast:	n/a	n/a
26	CTCF	chr4:122292000-122292150	BE2_C	brain:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
27	CTCF	chr4:122292000-122292150	GM12868	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
28	CTCF	chr4:122291971-122292181	GM13977	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
29	CTCF	chr4:122291930-122292195	HepG2	liver:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
30	CTCF	chr4:122291980-122292130	AG09309	skin:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
31	CTCF	chr4:122291980-122292130	GM12874	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
32	CTCF	chr4:122291699-122291825	GM12891	blood:	n/a	n/a
33	CTCF	chr4:122291730-122291783	Fibrobl	skin:	n/a	n/a
34	CTCF	chr4:122292000-122292150	HPF	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
35	CTCF	chr4:122291580-122291730	HFF	foreskin:	n/a	n/a
36	CTCF	chr4:122291954-122292184	LNCaP	prostate:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
37	CTCF	chr4:122291340-122291490	SAEC	small airway:	n/a	n/a
38	CTCF	chr4:122292020-122292170	HBMEC	blood vessel:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
39	CTCF	chr4:122291964-122292187	Spleen_OC	spleen:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
40	CTCF	chr4:122291980-122292130	AG09319	gingival:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
41	CTCF	chr4:122291995-122292139	ECC-1	luminal epithelium:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
42	CTCF	chr4:122291977-122292183	Pancreas_OC	pancreas:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
43	CTCF	chr4:122292080-122292230	HFF-Myc	foreskin:	n/a	n/a
44	CTCF	chr4:122292000-122292150	NHDF-neo	bronchial:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
45	CTCF	chr4:122291680-122291830	BJ	skin:	n/a	n/a
46	CTCF	chr4:122292020-122292170	HEEpiC	esophagus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
47	CTCF	chr4:122291940-122292090	HCPEpiC	choroid plexus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089
48	CTCF	chr4:122291960-122292110	GM12865	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
49	CTCF	chr4:122291260-122291410	AG09319	gingival:	n/a	n/a
50	CTCF	chr4:122291680-122291842	GM19238	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:122198899..122199696-chr4:122292166..122292719,2	MCF-7	breast:
2	chr4:122265924..122266538-chr4:122292160..122292685,2	MCF-7	breast:
3	chr4:122291624..122292430-chr4:122342879..122343479,3	MCF-7	breast:
4	chr4:122291642..122292373-chr4:122577439..122577960,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNIP3-2	chr4:122290588-122291500	NONHSAT098140

Variant related genes	Relation type
ENSG00000213480	TF binding region

Extended variants
information (count: 448 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:448 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12507798	chr4:122281488-122281489	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs187530152	chr4:122281534-122281535	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs561515472	chr4:122281557-122281558	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs368783385	chr4:122281567-122281568	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs28716099	chr4:122281621-122281622	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs546692996	chr4:122281635-122281636	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs547159668	chr4:122281669-122281670	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs567478770	chr4:122281676-122281677	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs543419009	chr4:122281686-122281687	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs138300390	chr4:122281730-122281731	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs556286229	chr4:122281731-122281732	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs575937394	chr4:122281732-122281733	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs538518541	chr4:122281740-122281741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs557747396	chr4:122281843-122281844	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs577601463	chr4:122281912-122281913	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs41422451	chr4:122281973-122281974	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs62319044	chr4:122281991-122281992	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs574215339	chr4:122282049-122282050	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs369682457	chr4:122282054-122282055	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs563023808	chr4:122282064-122282065	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs16997669	chr4:122282080-122282081	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs68079620	chr4:122282161-122282162	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs564905987	chr4:122282239-122282240	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs71602329	chr4:122282248-122282249	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs547513986	chr4:122282262-122282263	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs115259588	chr4:122282263-122282264	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs143840665	chr4:122282271-122282272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs549733691	chr4:122282272-122282273	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs569480971	chr4:122282273-122282274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs538583129	chr4:122282297-122282298	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs71602330	chr4:122282306-122282307	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs571353870	chr4:122282369-122282370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs533932892	chr4:122282397-122282398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs554094670	chr4:122282409-122282410	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs574053687	chr4:122282426-122282427	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs543079281	chr4:122282473-122282474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs192344414	chr4:122282475-122282476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs576692555	chr4:122282483-122282484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs545742398	chr4:122282487-122282488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs13122399	chr4:122282512-122282513	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs147236036	chr4:122282558-122282559	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs184142167	chr4:122282570-122282571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs139162474	chr4:122282576-122282577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs529769115	chr4:122282577-122282578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs549452560	chr4:122282585-122282586	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs73845781	chr4:122282590-122282591	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs114502637	chr4:122282625-122282626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs143085924	chr4:122282636-122282637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs116514471	chr4:122282650-122282651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs74822219	chr4:122282725-122282726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:73)

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
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	18350619	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
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Esophageal cancer	21851588	CNVD
Colorectal cancer	16272173	CNVD
Testicular germ cell tumor	18059402	CNVD
Ovarian cancer	22174824	CNVD
Neuroblastoma	21899760	CNVD
Renal cell carcinoma	18194544	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Myelofibrosis	22110671	CNVD
small cell lung cancer	20016488	CNVD
Clear cell renal cell carcinoma	18791270	CNVD
Acute myeloid leukemia	19651601	CNVD
Gastric cancer	16891809	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122280200-122281400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr4:122280200-122281600	Weak transcription	NHEK	skin
3	chr4:122280400-122281400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:122280400-122281400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:122280400-122281600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:122280400-122281600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:122281000-122282200	Enhancers	HMEC	breast
8	chr4:122281200-122282200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:122281200-122282200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr4:122281200-122283400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:122281400-122282200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:122281400-122282200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:122281600-122281800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:122281600-122282200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:122281600-122282200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:122281600-122282200	Enhancers	NHEK	skin
17	chr4:122282200-122294000	Weak transcription	HMEC	breast
18	chr4:122282200-122295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:122283400-122284000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:122287600-122288400	Enhancers	Left Ventricle	heart
21	chr4:122290600-122290800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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