Variant report

Variant	nsv1001654
Chromosome Location	chr4:122282456-122297539
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	ATF3	chr4:122297220-122297606	HCT-116	colon:	n/a	n/a
3	CBX3	chr4:122297146-122297654	HCT-116	colon:	n/a	n/a
4	CBX3	chr4:122297242-122297685	HCT-116	colon:	n/a	n/a
5	CEBPB	chr4:122296462-122296778	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr4:122296251-122296905	HCT-116	colon:	n/a	n/a
7	CEBPB	chr4:122296277-122296972	HCT-116	colon:	n/a	n/a
8	CEBPB	chr4:122288309-122288515	HepG2	liver:	n/a	chr4:122288383-122288394
9	CTCF	chr4:122291920-122292070	HCM	heart:	n/a	n/a
10	CTCF	chr4:122291696-122291780	A549	lung:	n/a	n/a
11	CTCF	chr4:122291920-122292070	HAc	cerebellar:	n/a	n/a
12	CTCF	chr4:122292000-122292150	GM12868	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
13	CTCF	chr4:122291980-122292130	GM12874	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
14	CTCF	chr4:122291592-122292410	A549	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
15	CTCF	chr4:122291600-122291750	GM12867	blood:	n/a	n/a
16	CTCF	chr4:122291940-122292090	HRE	kidney:	n/a	chr4:122292074-122292087 chr4:122292071-122292089
17	CTCF	chr4:122292020-122292170	RPTEC	kidney:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
18	CTCF	chr4:122291560-122291710	WI-38	lung:	n/a	n/a
19	CTCF	chr4:122291944-122292182	LNCaP	prostate:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
20	CTCF	chr4:122292000-122292150	HCT-116	colon:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
21	CTCF	chr4:122292020-122292170	HBMEC	blood vessel:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
22	CTCF	chr4:122292000-122292150	HRPEpiC	eye:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
23	CTCF	chr4:122291940-122292090	GM12865	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089
24	CTCF	chr4:122291940-122292090	HCM	heart:	n/a	chr4:122292074-122292087 chr4:122292071-122292089
25	CTCF	chr4:122292000-122292150	NB4	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
26	CTCF	chr4:122292020-122292170	GM12878	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
27	CTCF	chr4:122292030-122292108	GM20000	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
28	CTCF	chr4:122291980-122292130	A549	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
29	CTCF	chr4:122292000-122292150	Hela-S3	cervix:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
30	CTCF	chr4:122293300-122293450	GM12873	blood:	n/a	n/a
31	CTCF	chr4:122291920-122292187	K562	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
32	CTCF	chr4:122291980-122292130	GM12869	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
33	CTCF	chr4:122292000-122292150	HPF	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
34	CTCF	chr4:122291960-122292110	HEEpiC	esophagus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
35	CTCF	chr4:122292013-122292139	MCF-7	breast:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
36	CTCF	chr4:122292600-122292750	NHLF	lung:	n/a	n/a
37	CTCF	chr4:122290640-122290708	Fibrobl	skin:	n/a	n/a
38	CTCF	chr4:122291580-122291730	GM12865	blood:	n/a	n/a
39	CTCF	chr4:122292000-122292150	HA-sp	spinal cord:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
40	CTCF	chr4:122291980-122292130	GM12871	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
41	CTCF	chr4:122292080-122292230	MCF-7	breast:	n/a	n/a
42	CTCF	chr4:122291972-122292202	Lung_OC	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
43	CTCF	chr4:122291980-122292130	SAEC	small airway:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
44	CTCF	chr4:122291980-122292130	GM06990	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
45	CTCF	chr4:122292020-122292170	HRPEpiC	eye:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
46	CTCF	chr4:122292020-122292170	HMF	breast:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
47	CTCF	chr4:122292020-122292170	HCPEpiC	choroid plexus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
48	CTCF	chr4:122291937-122292210	HepG2	liver:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
49	CTCF	chr4:122292620-122292770	GM12873	blood:	n/a	n/a
50	CTCF	chr4:122292000-122292150	AG10803	skin:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094

No.	Distal block	Cell Line	Cell type
1	chr4:122290131..122292541-chr4:122296588..122298243,2	K562	blood:
2	chr4:122291624..122292430-chr4:122342879..122343479,3	MCF-7	breast:
3	chr4:122265924..122266538-chr4:122292160..122292685,2	MCF-7	breast:
4	chr4:122291642..122292373-chr4:122577439..122577960,2	MCF-7	breast:
5	chr4:122198899..122199696-chr4:122292166..122292719,2	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
ENSG00000213480	chromatin interactions

Extended variants
information (count: 621 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:621 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543079281	chr4:122282473-122282474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs192344414	chr4:122282475-122282476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs576692555	chr4:122282483-122282484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs545742398	chr4:122282487-122282488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs13122399	chr4:122282512-122282513	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs147236036	chr4:122282558-122282559	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs184142167	chr4:122282570-122282571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs139162474	chr4:122282576-122282577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs529769115	chr4:122282577-122282578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs549452560	chr4:122282585-122282586	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs73845781	chr4:122282590-122282591	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs114502637	chr4:122282625-122282626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs143085924	chr4:122282636-122282637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs116514471	chr4:122282650-122282651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs74822219	chr4:122282725-122282726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs553899432	chr4:122282755-122282756	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs77285108	chr4:122282768-122282769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs35150174	chr4:122282775-122282776	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs72917765	chr4:122282794-122282795	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs188406741	chr4:122282829-122282830	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs148663730	chr4:122282845-122282846	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs17051343	chr4:122282857-122282858	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs570802872	chr4:122282865-122282866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs17372496	chr4:122282918-122282919	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs541678953	chr4:122282919-122282920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs142141870	chr4:122282935-122282936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs547122113	chr4:122282949-122282950	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs17372524	chr4:122282972-122282973	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs35555943	chr4:122283004-122283005	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs575881791	chr4:122283020-122283021	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs375245756	chr4:122283101-122283102	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs192234771	chr4:122283241-122283242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs10433907	chr4:122283253-122283254	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs150800839	chr4:122283254-122283255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs551955529	chr4:122283303-122283304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs113854495	chr4:122283333-122283334	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs565837639	chr4:122283369-122283370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs139182141	chr4:122283423-122283424	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs536994228	chr4:122283431-122283432	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs34325960	chr4:122283475-122283476	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs35906974	chr4:122283506-122283507	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs11726005	chr4:122283523-122283524	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs184570643	chr4:122283525-122283526	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs550336368	chr4:122283575-122283576	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs190246680	chr4:122283591-122283592	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs116345218	chr4:122283608-122283609	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs62319045	chr4:122283617-122283618	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs572587620	chr4:122283639-122283640	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs112927828	chr4:122283656-122283657	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs144001861	chr4:122283680-122283681	Enhancers 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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122281200-122283400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:122282200-122294000	Weak transcription	HMEC	breast
3	chr4:122282200-122295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:122283400-122284000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:122287600-122288400	Enhancers	Left Ventricle	heart
6	chr4:122290600-122290800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:122294000-122294200	Enhancers	HMEC	breast
8	chr4:122294000-122294800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr4:122294200-122294600	Weak transcription	HMEC	breast
10	chr4:122294600-122295000	Enhancers	HMEC	breast
11	chr4:122294800-122295200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:122294800-122298800	Enhancers	NHEK	skin
13	chr4:122295000-122295400	Flanking Active TSS	HMEC	breast
14	chr4:122295000-122295800	Enhancers	Fetal Lung	lung
15	chr4:122295200-122297600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:122295200-122299000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr4:122295400-122296000	Enhancers	HMEC	breast
18	chr4:122295400-122297600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:122295600-122299400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:122295800-122297000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:122295800-122297600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:122296000-122296200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr4:122296000-122296200	Enhancers	Fetal Muscle Leg	muscle
24	chr4:122296000-122296200	Flanking Active TSS	HMEC	breast
25	chr4:122296000-122296400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:122296000-122296600	Enhancers	Right Ventricle	heart
27	chr4:122296200-122296400	Enhancers	Fetal Intestine Large	intestine
28	chr4:122296200-122296400	Enhancers	HMEC	breast
29	chr4:122296200-122296400	Bivalent Enhancer	NHDF-Ad	bronchial
30	chr4:122296200-122296800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:122296200-122296800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr4:122296200-122297200	Enhancers	Hela-S3	cervix
33	chr4:122296400-122296600	Flanking Active TSS	HMEC	breast
34	chr4:122296400-122301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:122296600-122299200	Enhancers	HMEC	breast
36	chr4:122296600-122300800	Weak transcription	Right Ventricle	heart

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