Variant report

Variant	nsv596049
Chromosome Location	chr4:166128515-166129093
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	chr4:166128621-166128911	HepG2	liver:	n/a	n/a
2	ARID3A	chr4:166129030-166129091	K562	blood:	n/a	n/a
3	ARID3A	chr4:166128689-166128731	K562	blood:	n/a	n/a
4	ATF1	chr4:166128531-166128845	K562	blood:	n/a	n/a
5	ATF3	chr4:166128608-166128920	K562	blood:	n/a	n/a
6	ATF3	chr4:166128654-166128843	GM12878	blood:	n/a	n/a
7	BACH1	chr4:166129092-166129306	H1-hESC	embryonic stem cell:	n/a	n/a
8	BHLHE40	chr4:166128688-166129218	K562	blood:	n/a	chr4:166129145-166129161 chr4:166128730-166128746 chr4:166129150-166129166 chr4:166128955-166128971 chr4:166128910-166128926 chr4:166128729-166128745 chr4:166129099-166129115 chr4:166129142-166129158
9	BHLHE40	chr4:166128304-166129269	GM12878	blood:	n/a	chr4:166129145-166129161 chr4:166128730-166128746 chr4:166129150-166129166 chr4:166128955-166128971 chr4:166128910-166128926 chr4:166128729-166128745 chr4:166129099-166129115 chr4:166129142-166129158
10	CCNT2	chr4:166128393-166129240	K562	blood:	n/a	n/a
11	CEBPD	chr4:166128437-166128893	HepG2	liver:	n/a	n/a
12	CHD1	chr4:166129054-166129055	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr4:166128381-166129193	Hela-S3	cervix:	n/a	chr4:166129156-166129166
14	CREB1	chr4:166128422-166129405	GM12878	blood:	n/a	n/a
15	CREB1	chr4:166128426-166128913	K562	blood:	n/a	n/a
16	CREB1	chr4:166128471-166128989	HepG2	liver:	n/a	n/a
17	CREB1	chr4:166128401-166129030	K562	blood:	n/a	n/a
18	CREB1	chr4:166128405-166128979	A549	lung:	n/a	n/a
19	CREB1	chr4:166128572-166128887	A549	lung:	n/a	n/a
20	CREB1	chr4:166128473-166128990	H1-hESC	embryonic stem cell:	n/a	n/a
21	CREB1	chr4:166128056-166129241	HepG2	liver:	n/a	n/a
22	CREB1	chr4:166128418-166128980	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTBP2	chr4:166128291-166129366	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr4:166128920-166128935	LNCaP	prostate:	n/a	n/a
25	CTCF	chr4:166128858-166128986	MCF-7	breast:	n/a	chr4:166128909-166128922
26	CTCF	chr4:166128820-166128970	GM12864	blood:	n/a	chr4:166128909-166128922
27	CTCF	chr4:166128876-166128948	GM10248	blood:	n/a	chr4:166128909-166128922
28	CTCF	chr4:166128844-166129003	GM19239	blood:	n/a	chr4:166128909-166128922
29	CTCF	chr4:166128820-166128970	GM12866	blood:	n/a	chr4:166128909-166128922
30	CTCF	chr4:166128840-166128990	GM12868	blood:	n/a	chr4:166128909-166128922
31	CTCF	chr4:166128780-166128930	AG04449	skin:	n/a	chr4:166128909-166128922
32	CTCF	chr4:166128888-166128953	NHEK	skin:	n/a	chr4:166128909-166128922
33	CTCF	chr4:166128820-166128970	HMEC	breast:	n/a	chr4:166128909-166128922
34	CTCF	chr4:166128800-166128950	GM12875	blood:	n/a	chr4:166128909-166128922
35	CTCF	chr4:166128844-166129001	GM19238	blood:	n/a	chr4:166128909-166128922
36	CTCF	chr4:166128800-166128950	SAEC	small airway:	n/a	chr4:166128909-166128922
37	CTCF	chr4:166128850-166128981	GM12891	blood:	n/a	chr4:166128909-166128922
38	CTCF	chr4:166128638-166129084	GM12878	blood:	n/a	chr4:166128909-166128922
39	CTCF	chr4:166129023-166129028	MCF-7	breast:	n/a	n/a
40	CTCF	chr4:166128756-166128978	HepG2	liver:	n/a	chr4:166128909-166128922
41	CTCF	chr4:166128900-166129050	K562	blood:	n/a	chr4:166128909-166128922
42	CTCF	chr4:166128853-166129001	GM12892	blood:	n/a	chr4:166128909-166128922
43	CTCF	chr4:166128800-166128950	WERI-Rb-1	eye:	n/a	chr4:166128909-166128922
44	CTCF	chr4:166128840-166128990	SK-N-SH_RA	brain:	n/a	chr4:166128909-166128922
45	CTCF	chr4:166128980-166129130	GM12870	blood:	n/a	n/a
46	CTCF	chr4:166128860-166129010	GM12874	blood:	n/a	chr4:166128909-166128922
47	CTCF	chr4:166129040-166129190	AG04449	skin:	n/a	chr4:166129154-166129167
48	CTCF	chr4:166128940-166129090	NHEK	skin:	n/a	n/a
49	CTCF	chr4:166128840-166128990	AG04449	skin:	n/a	chr4:166128909-166128922
50	CTCF	chr4:166128860-166129010	GM12866	blood:	n/a	chr4:166128909-166128922

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:166129003-166129053	SAEC	small airway:	n/a
2	chr4:166129003-166129053	GM12892	blood:	n/a
3	chr4:166129003-166129053	MCF-7	breast:	n/a
4	chr4:166128480-166128530	AoSMC	blood vessel:	n/a
5	chr4:166129003-166129053	Jurkat	blood:	n/a
6	chr4:166129003-166129053	MCF10A-Er-Src	breast:	n/a
7	chr4:166129003-166129053	U87	brain:	n/a
8	chr4:166129003-166129053	GM12891	blood:	n/a
9	chr4:166128480-166128530	ECC-1	luminal epithelium:	n/a
10	chr4:166128480-166128530	HNPCEpiC	eye:	n/a
11	chr4:166128480-166128530	NHDF-neo	bronchial:	n/a
12	chr4:166129003-166129053	K562	blood:	n/a
13	chr4:166128480-166128530	GM12891	blood:	n/a
14	chr4:166129003-166129053	ovcar-3	ovarian:	n/a
15	chr4:166128480-166128530	BJ	skin:	n/a
16	chr4:166129003-166129053	AG09319	gingival:	n/a
17	chr4:166129003-166129053	HRPEpiC	eye:	n/a
18	chr4:166128480-166128530	GM12878	blood:	n/a
19	chr4:166128480-166128530	SAEC	small airway:	n/a
20	chr4:166128480-166128530	PrEC	prostate:	n/a
21	chr4:166129003-166129053	HCM	heart:	n/a
22	chr4:166128480-166128530	HCT-116	colon:	n/a
23	chr4:166128480-166128530	T-47D	breast:	n/a
24	chr4:166128480-166128530	HEK293	kidney:	embryo
25	chr4:166128480-166128530	HCPEpiC	choroid plexus:	n/a
26	chr4:166129003-166129053	HL-60	blood:	n/a
27	chr4:166128480-166128530	GM06990	blood:	n/a
28	chr4:166128480-166128530	NH-A	brain:	n/a
29	chr4:166129003-166129053	BJ	skin:	n/a
30	chr4:166129003-166129053	IMR90	lung:	fetal
31	chr4:166128480-166128530	HRCEpiC	kidney:	n/a
32	chr4:166128480-166128530	U87	brain:	n/a
33	chr4:166128480-166128530	Caco-2	colon:	n/a
34	chr4:166128480-166128530	AG04450	lung:	fetal
35	chr4:166129003-166129053	Hela-S3	cervix:	n/a
36	chr4:166129003-166129053	HAEpiC	amniotic membrane:	n/a
37	chr4:166129003-166129053	NHBE	bronchial:	n/a
38	chr4:166128480-166128530	HRPEpiC	eye:	n/a
39	chr4:166128480-166128530	NHBE	bronchial:	n/a
40	chr4:166129003-166129053	ProgFib	skin:	n/a
41	chr4:166128480-166128530	ovcar-3	ovarian:	n/a
42	chr4:166129003-166129053	HIPEpiC	eye:	n/a
43	chr4:166129003-166129053	Caco-2	colon:	n/a
44	chr4:166129003-166129053	AoSMC	blood vessel:	n/a
45	chr4:166128480-166128530	HCF	heart:	n/a
46	chr4:166128480-166128530	GM12892	blood:	n/a
47	chr4:166129003-166129053	PrEC	prostate:	n/a
48	chr4:166128480-166128530	AG10803	skin:	n/a
49	chr4:166128480-166128530	HIPEpiC	eye:	n/a
50	chr4:166129003-166129053	HEK293	kidney:	embryo

No.	Distal block	Cell Line	Cell type
1	chr4:166126423..166128941-chr4:166299614..166301287,2	MCF-7	breast:
2	chr4:166126308..166130366-chr4:166247405..166251145,5	K562	blood:
3	chr4:166032812..166034984-chr4:166128697..166130341,2	K562	blood:
4	chr4:166127386..166130072-chr4:166247171..166250406,6	MCF-7	breast:
5	chr4:166127800..166130090-chr4:166130347..166132969,2	MCF-7	breast:
6	chr4:166127276..166130366-chr4:166247405..166250443,3	K562	blood:
7	chr4:166128531..166130929-chr4:166246215..166249595,5	MCF-7	breast:
8	chr4:166114045..166117632-chr4:166124756..166128607,4	K562	blood:

Variant related genes	Relation type
KLHL2	TF binding region
KLHL2	CpG island
ENSG00000052802	chromatin interactions
ENSG00000109472	chromatin interactions
ENSG00000109466	chromatin interactions
ENSG00000170088	chromatin interactions

Extended variants
information (count: 14 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs535535177	chr4:166128544-166128545	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs557068904	chr4:166128554-166128555	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs575541480	chr4:166128634-166128635	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs546637520	chr4:166128640-166128641	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs546226453	chr4:166128653-166128654	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs564577526	chr4:166128726-166128727	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs573491209	chr4:166128741-166128742	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs540795869	chr4:166128773-166128774	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs562245862	chr4:166128793-166128794	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs529545669	chr4:166128833-166128834	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs548295917	chr4:166128877-166128878	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs190204099	chr4:166128911-166128912	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs11547096	chr4:166128965-166128966	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs530377254	chr4:166128994-166128995	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:70)

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
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
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	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
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	16272173	CNVD
Breast cancer	17133270	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
Testicular germ cell tumor	18059402	CNVD
Ovarian cancer	22174824	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	21785460	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Ewing''s sarcoma	17952124	CNVD
Breast cancer	21633010	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20581869	CNVD
Glioblastoma multiforme	22286061	CNVD
Basal cell lymphoma	17053054	CNVD
Hepatocellular carcinoma	16750200	CNVD
Colorectal cancer	16774939	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Myelofibrosis	22110671	CNVD
intellectual deficit	22127048	CNVD
abnormal development	18461090	CNVD

Chromatin state (count:143 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166127600-166128600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:166127600-166128600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr4:166127600-166129200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:166127600-166129400	Active TSS	Hela-S3	cervix
5	chr4:166127600-166129800	Active TSS	Colonic Mucosa	Colon
6	chr4:166127800-166128600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:166127800-166129800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:166127800-166129800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:166127800-166129800	Active TSS	Ovary	ovary
10	chr4:166127800-166130200	Active TSS	Psoas Muscle	Psoas
11	chr4:166127800-166130400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr4:166128000-166129000	Active TSS	Brain Germinal Matrix	brain
13	chr4:166128000-166129200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:166128000-166129600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:166128000-166129600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:166128000-166129600	Active TSS	Gastric	stomach
17	chr4:166128000-166130000	Active TSS	Brain Hippocampus Middle	brain
18	chr4:166128000-166130000	Active TSS	A549	lung
19	chr4:166128000-166130200	Active TSS	Aorta	Aorta
20	chr4:166128000-166130200	Active TSS	Left Ventricle	heart
21	chr4:166128000-166130200	Active TSS	Right Ventricle	heart
22	chr4:166128000-166130200	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr4:166128000-166130600	Active TSS	Lung	lung
24	chr4:166128000-166131400	Active TSS	Esophagus	oesophagus
25	chr4:166128200-166128800	Active TSS	H1 Cell Line	embryonic stem cell
26	chr4:166128200-166129000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:166128200-166129000	Active TSS	Thymus	Thymus
28	chr4:166128200-166129200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr4:166128200-166129200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:166128200-166129400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:166128200-166129400	Active TSS	Primary B cells from cord blood	blood
32	chr4:166128200-166129400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:166128200-166129400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr4:166128200-166129400	Active TSS	Fetal Intestine Large	intestine
35	chr4:166128200-166129400	Transcr. at gene 5' and 3'	Right Atrium	heart
36	chr4:166128200-166129600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:166128200-166129600	Active TSS	Colon Smooth Muscle	Colon
38	chr4:166128200-166129600	Active TSS	Small Intestine	intestine
39	chr4:166128200-166129800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:166128200-166129800	Active TSS	Placenta Amnion	Placenta Amnion
41	chr4:166128200-166130000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:166128200-166130000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:166128200-166130000	Active TSS	Brain Cingulate Gyrus	brain
44	chr4:166128200-166130000	Active TSS	Rectal Smooth Muscle	rectum
45	chr4:166128200-166130200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:166128200-166130200	Active TSS	NHLF	lung
47	chr4:166128200-166130400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr4:166128200-166130400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr4:166128200-166130400	Active TSS	Brain Anterior Caudate	brain
50	chr4:166128200-166130400	Active TSS	Rectal Mucosa Donor 29	rectum

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