Variant report

Variant	nsv1003477
Chromosome Location	chr4:122281973-122297539
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	chr4:122296277-122296972	HCT-116	colon:	n/a	n/a
6	CEBPB	chr4:122296462-122296778	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr4:122296251-122296905	HCT-116	colon:	n/a	n/a
8	CEBPB	chr4:122288309-122288515	HepG2	liver:	n/a	chr4:122288383-122288394
9	CTCF	chr4:122292000-122292150	HPF	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
10	CTCF	chr4:122292000-122292150	AG09319	gingival:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
11	CTCF	chr4:122291980-122292130	HCFaa	heart:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
12	CTCF	chr4:122291920-122292187	K562	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
13	CTCF	chr4:122291980-122292130	GM12866	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
14	CTCF	chr4:122292020-122292170	HBMEC	blood vessel:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
15	CTCF	chr4:122291715-122291789	LNCaP	prostate:	n/a	n/a
16	CTCF	chr4:122291985-122292180	Kidney_OC	kidney:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
17	CTCF	chr4:122291980-122292130	AG09309	skin:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
18	CTCF	chr4:122291394-122291460	GM12891	blood:	n/a	n/a
19	CTCF	chr4:122291699-122291825	GM12891	blood:	n/a	n/a
20	CTCF	chr4:122292080-122292230	MCF-7	breast:	n/a	n/a
21	CTCF	chr4:122292000-122292150	GM12867	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
22	CTCF	chr4:122291600-122291750	GM12867	blood:	n/a	n/a
23	CTCF	chr4:122291960-122292193	GM12878	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
24	CTCF	chr4:122292060-122292210	NHEK	skin:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
25	CTCF	chr4:122292000-122292150	AoAF	blood vessel:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
26	CTCF	chr4:122291937-122292210	HepG2	liver:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
27	CTCF	chr4:122292000-122292150	HCT-116	colon:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
28	CTCF	chr4:122291951-122292204	SK-N-SH_RA	brain:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
29	CTCF	chr4:122291937-122292194	A549	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
30	CTCF	chr4:122292100-122292250	HMEC	breast:	n/a	n/a
31	CTCF	chr4:122292020-122292170	AG09309	skin:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
32	CTCF	chr4:122291900-122292050	HMEC	breast:	n/a	n/a
33	CTCF	chr4:122291980-122292130	HEK293	kidney:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
34	CTCF	chr4:122292007-122292176	Gliobla	brain:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
35	CTCF	chr4:122291960-122292110	GM12865	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
36	CTCF	chr4:122291960-122292110	HEEpiC	esophagus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
37	CTCF	chr4:122292000-122292150	HVMF	connective:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
38	CTCF	chr4:122292000-122292150	BE2_C	brain:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
39	CTCF	chr4:122292020-122292170	HEEpiC	esophagus:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
40	CTCF	chr4:122291960-122292110	GM12878	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
41	CTCF	chr4:122291980-122292130	AG04450	lung:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
42	CTCF	chr4:122291960-122292110	GM12874	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
43	CTCF	chr4:122291920-122292070	HAc	cerebellar:	n/a	n/a
44	CTCF	chr4:122291560-122291710	RPTEC	kidney:	n/a	n/a
45	CTCF	chr4:122291878-122292266	GM12878	blood:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
46	CTCF	chr4:122290900-122291050	NHDF-neo	bronchial:	n/a	n/a
47	CTCF	chr4:122291920-122292070	WERI-Rb-1	eye:	n/a	n/a
48	CTCF	chr4:122291220-122291370	GM12865	blood:	n/a	n/a
49	CTCF	chr4:122292060-122292210	BE2_C	brain:	n/a	chr4:122292074-122292087 chr4:122292071-122292089 chr4:122292073-122292094
50	CTCF	chr4:122291980-122292130	GM12874	blood:	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	chr4:122265924..122266538-chr4:122292160..122292685,2	MCF-7	breast:
3	chr4:122291642..122292373-chr4:122577439..122577960,2	MCF-7	breast:
4	chr4:122198899..122199696-chr4:122292166..122292719,2	MCF-7	breast:
5	chr4:122291624..122292430-chr4:122342879..122343479,3	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: 641 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:641 , 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	rs41422451	chr4:122281973-122281974	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs62319044	chr4:122281991-122281992	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs574215339	chr4:122282049-122282050	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs369682457	chr4:122282054-122282055	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs563023808	chr4:122282064-122282065	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs16997669	chr4:122282080-122282081	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs68079620	chr4:122282161-122282162	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs564905987	chr4:122282239-122282240	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs71602329	chr4:122282248-122282249	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs547513986	chr4:122282262-122282263	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs115259588	chr4:122282263-122282264	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs143840665	chr4:122282271-122282272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs549733691	chr4:122282272-122282273	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs569480971	chr4:122282273-122282274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs538583129	chr4:122282297-122282298	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs71602330	chr4:122282306-122282307	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs571353870	chr4:122282369-122282370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs533932892	chr4:122282397-122282398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs554094670	chr4:122282409-122282410	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs574053687	chr4:122282426-122282427	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs543079281	chr4:122282473-122282474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs192344414	chr4:122282475-122282476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs576692555	chr4:122282483-122282484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs545742398	chr4:122282487-122282488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs13122399	chr4:122282512-122282513	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs147236036	chr4:122282558-122282559	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs184142167	chr4:122282570-122282571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs139162474	chr4:122282576-122282577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs529769115	chr4:122282577-122282578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs549452560	chr4:122282585-122282586	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs73845781	chr4:122282590-122282591	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs114502637	chr4:122282625-122282626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs143085924	chr4:122282636-122282637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs116514471	chr4:122282650-122282651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs74822219	chr4:122282725-122282726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs553899432	chr4:122282755-122282756	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs77285108	chr4:122282768-122282769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs35150174	chr4:122282775-122282776	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
39	rs72917765	chr4:122282794-122282795	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs188406741	chr4:122282829-122282830	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs148663730	chr4:122282845-122282846	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs17051343	chr4:122282857-122282858	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs570802872	chr4:122282865-122282866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs17372496	chr4:122282918-122282919	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs541678953	chr4:122282919-122282920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs142141870	chr4:122282935-122282936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs547122113	chr4:122282949-122282950	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs17372524	chr4:122282972-122282973	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs35555943	chr4:122283004-122283005	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs575881791	chr4:122283020-122283021	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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122281000-122282200	Enhancers	HMEC	breast
2	chr4:122281200-122282200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:122281200-122282200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr4:122281200-122283400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:122281400-122282200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:122281400-122282200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:122281600-122282200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:122281600-122282200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr4:122281600-122282200	Enhancers	NHEK	skin
10	chr4:122282200-122294000	Weak transcription	HMEC	breast
11	chr4:122282200-122295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:122283400-122284000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:122287600-122288400	Enhancers	Left Ventricle	heart
14	chr4:122290600-122290800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:122294000-122294200	Enhancers	HMEC	breast
16	chr4:122294000-122294800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr4:122294200-122294600	Weak transcription	HMEC	breast
18	chr4:122294600-122295000	Enhancers	HMEC	breast
19	chr4:122294800-122295200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:122294800-122298800	Enhancers	NHEK	skin
21	chr4:122295000-122295400	Flanking Active TSS	HMEC	breast
22	chr4:122295000-122295800	Enhancers	Fetal Lung	lung
23	chr4:122295200-122297600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:122295200-122299000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:122295400-122296000	Enhancers	HMEC	breast
26	chr4:122295400-122297600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:122295600-122299400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:122295800-122297000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:122295800-122297600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:122296000-122296200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr4:122296000-122296200	Enhancers	Fetal Muscle Leg	muscle
32	chr4:122296000-122296200	Flanking Active TSS	HMEC	breast
33	chr4:122296000-122296400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:122296000-122296600	Enhancers	Right Ventricle	heart
35	chr4:122296200-122296400	Enhancers	Fetal Intestine Large	intestine
36	chr4:122296200-122296400	Enhancers	HMEC	breast
37	chr4:122296200-122296400	Bivalent Enhancer	NHDF-Ad	bronchial
38	chr4:122296200-122296800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:122296200-122296800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:122296200-122297200	Enhancers	Hela-S3	cervix
41	chr4:122296400-122296600	Flanking Active TSS	HMEC	breast
42	chr4:122296400-122301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:122296600-122299200	Enhancers	HMEC	breast
44	chr4:122296600-122300800	Weak transcription	Right Ventricle	heart

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