Variant report

Variant	nsv572548
Chromosome Location	chr16:48418557-48419495
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	chr16:48419367-48419551	K562	blood:	n/a	n/a
2	ARID3A	chr16:48419130-48419530	HepG2	liver:	n/a	n/a
3	ATF3	chr16:48419311-48419585	HepG2	liver:	n/a	chr16:48419332-48419341 chr16:48419408-48419417
4	BCL3	chr16:48419341-48419762	A549	lung:	n/a	chr16:48419710-48419723 chr16:48419361-48419370 chr16:48419359-48419372 chr16:48419712-48419725 chr16:48419715-48419724 chr16:48419712-48419721 chr16:48419623-48419636
5	BCL3	chr16:48419028-48419378	GM12878	blood:	n/a	chr16:48419327-48419340 chr16:48419361-48419370 chr16:48419359-48419372
6	BCLAF1	chr16:48419242-48419765	GM12878	blood:	n/a	chr16:48419710-48419723 chr16:48419327-48419340 chr16:48419361-48419370 chr16:48419359-48419372 chr16:48419712-48419725 chr16:48419715-48419724 chr16:48419712-48419721 chr16:48419623-48419636
7	BHLHE40	chr16:48418075-48419797	GM12878	blood:	n/a	chr16:48419664-48419680 chr16:48419620-48419636 chr16:48418657-48418673
8	BHLHE40	chr16:48417882-48419832	HepG2	liver:	n/a	chr16:48419664-48419680 chr16:48419620-48419636 chr16:48418657-48418673
9	BHLHE40	chr16:48417811-48420020	K562	blood:	n/a	chr16:48419664-48419680 chr16:48419620-48419636 chr16:48418657-48418673
10	BHLHE40	chr16:48418641-48418772	A549	lung:	n/a	chr16:48418657-48418673
11	BRCA1	chr16:48419426-48419579	H1-hESC	embryonic stem cell:	n/a	n/a
12	CCNT2	chr16:48418457-48419867	K562	blood:	n/a	chr16:48418561-48418570 chr16:48419837-48419846 chr16:48418924-48418933 chr16:48419408-48419417 chr16:48418929-48418938
13	CEBPB	chr16:48419310-48419610	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr16:48418494-48418583	Hela-S3	cervix:	n/a	n/a
15	CEBPD	chr16:48418443-48418750	HepG2	liver:	n/a	n/a
16	CEBPD	chr16:48419182-48419804	HepG2	liver:	n/a	n/a
17	CEBPD	chr16:48418771-48419821	HepG2	liver:	n/a	n/a
18	CHD1	chr16:48418974-48419965	GM12878	blood:	n/a	chr16:48419623-48419633 chr16:48418977-48418984
19	CHD1	chr16:48418999-48419289	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD1	chr16:48418594-48418677	GM12878	blood:	n/a	n/a
21	CHD1	chr16:48418054-48418654	H1-hESC	embryonic stem cell:	n/a	n/a
22	CHD2	chr16:48417705-48418715	Hela-S3	cervix:	n/a	n/a
23	CHD2	chr16:48419431-48419915	HepG2	liver:	n/a	chr16:48419623-48419633
24	CHD2	chr16:48419032-48419232	GM12878	blood:	n/a	n/a
25	CHD2	chr16:48418956-48420102	Hela-S3	cervix:	n/a	chr16:48419623-48419633 chr16:48418977-48418984
26	CHD2	chr16:48418074-48418559	K562	blood:	n/a	n/a
27	CHD2	chr16:48419447-48419985	H1-hESC	embryonic stem cell:	n/a	chr16:48419623-48419633
28	CHD2	chr16:48418430-48418627	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD2	chr16:48418969-48419747	K562	blood:	n/a	chr16:48419623-48419633 chr16:48418977-48418984
30	CREB1	chr16:48418838-48419718	A549	lung:	n/a	n/a
31	CTBP2	chr16:48419480-48419969	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr16:48419480-48419630	GM12875	blood:	n/a	n/a
33	CTCF	chr16:48419440-48419590	GM12874	blood:	n/a	n/a
34	CTCF	chr16:48419096-48419630	GM12878	blood:	n/a	n/a
35	CTCF	chr16:48419240-48419390	HMEC	breast:	n/a	n/a
36	CTCF	chr16:48419460-48419610	GM12868	blood:	n/a	n/a
37	CTCF	chr16:48419495-48419548	GM19239	blood:	n/a	n/a
38	CTCF	chr16:48419360-48419510	AG04449	skin:	n/a	n/a
39	CTCF	chr16:48419420-48419570	HepG2	liver:	n/a	n/a
40	CTCF	chr16:48419480-48419630	HUVEC	blood vessel:	n/a	n/a
41	CTCF	chr16:48419215-48419218	MCF-7	breast:	n/a	n/a
42	CTCF	chr16:48419159-48419205	MCF-7	breast:	n/a	n/a
43	CTCF	chr16:48419338-48419503	Spleen_OC	spleen:	n/a	n/a
44	CTCF	chr16:48419400-48419550	GM12871	blood:	n/a	n/a
45	CTCF	chr16:48419325-48419386	GM10266	blood:	n/a	n/a
46	CTCF	chr16:48419460-48419610	SK-N-SH_RA	brain:	n/a	n/a
47	E2F1	chr16:48418486-48419865	Hela-S3	cervix:	n/a	chr16:48419361-48419371 chr16:48419711-48419721 chr16:48419419-48419427 chr16:48419311-48419318 chr16:48419408-48419417 chr16:48419311-48419318 chr16:48419418-48419429 chr16:48418977-48418984 chr16:48419377-48419386 chr16:48419311-48419319 chr16:48419418-48419428 chr16:48419419-48419427 chr16:48419429-48419438 chr16:48419311-48419318 chr16:48419311-48419319 chr16:48419334-48419343
48	E2F4	chr16:48418349-48419812	K562	blood:	n/a	chr16:48419361-48419371 chr16:48419711-48419721 chr16:48419419-48419427 chr16:48419311-48419318 chr16:48419408-48419417 chr16:48419311-48419318 chr16:48419418-48419429 chr16:48418977-48418984 chr16:48419377-48419386 chr16:48419311-48419319 chr16:48419418-48419428 chr16:48419419-48419427 chr16:48419429-48419438 chr16:48419311-48419318 chr16:48419311-48419319 chr16:48419334-48419343
49	E2F4	chr16:48418928-48420047	MCF10A-Er-Src	breast:	n/a	chr16:48419361-48419371 chr16:48419711-48419721 chr16:48419419-48419427 chr16:48419311-48419318 chr16:48419408-48419417 chr16:48419311-48419318 chr16:48419418-48419429 chr16:48418977-48418984 chr16:48419377-48419386 chr16:48419311-48419319 chr16:48419418-48419428 chr16:48419419-48419427 chr16:48419429-48419438 chr16:48419311-48419318 chr16:48419311-48419319 chr16:48419334-48419343
50	E2F6	chr16:48419315-48420124	H1-hESC	embryonic stem cell:	n/a	chr16:48419361-48419371 chr16:48419711-48419721 chr16:48419419-48419427 chr16:48419408-48419417 chr16:48419418-48419429 chr16:48419377-48419386 chr16:48419418-48419428 chr16:48419419-48419427 chr16:48419429-48419438 chr16:48419334-48419343

No.	Distal block	Cell Line	Cell type
1	chr16:48380431..48382791-chr16:48417861..48420626,2	K562	blood:
2	chr1:212208566..212209259-chr16:48419035..48419960,2	Hela-S3	cervix:
3	chr16:48399845..48400801-chr16:48418367..48419048,2	Hela-S3	cervix:
4	chr16:48419410..48421944-chr16:48545496..48547470,2	MCF-7	breast:
5	chr16:48388703..48393705-chr16:48416034..48420195,6	K562	blood:
6	chr1:153508413..153509221-chr16:48418944..48419933,2	Hela-S3	cervix:
7	chr16:48416397..48419006-chr16:48635531..48637181,2	K562	blood:
8	chr16:48417747..48421302-chr16:48425164..48430136,6	K562	blood:
9	chr16:48398121..48402229-chr16:48414201..48420573,11	MCF-7	breast:
10	chr16:48418015..48420544-chr16:48643775..48645908,3	MCF-7	breast:
11	chr16:48419190..48419723-chr20:30194517..30195068,2	HCT-116	colon:
12	chr16:48417956..48420702-chr16:48642244..48644303,3	K562	blood:
13	chr12:57039442..57040047-chr16:48419364..48420064,2	Hela-S3	cervix:
14	chr16:48396253..48404408-chr16:48411826..48421166,27	K562	blood:
15	chr15:85291369..85292229-chr16:48418740..48419424,2	Hela-S3	cervix:
16	chr16:48418761..48419469-chr22:42228810..42229760,2	Hela-S3	cervix:
17	chr16:48277094..48279506-chr16:48417848..48419466,2	K562	blood:
18	chr12:7261155..7261904-chr16:48418914..48419874,2	Hela-S3	cervix:
19	chr16:2013351..2015357-chr16:48417776..48419360,2	MCF-7	breast:
20	chr16:48388635..48393801-chr16:48416034..48420195,7	K562	blood:
21	chr16:48419370..48419971-chr19:17515260..17516132,2	Hela-S3	cervix:
22	chr16:48419382..48420884-chr16:48422551..48425300,2	MCF-7	breast:
23	chr16:48392029..48394915-chr16:48416777..48418892,2	MCF-7	breast:
24	chr16:48418738..48419529-chr16:89626613..89627546,2	Hela-S3	cervix:
25	chr16:48397931..48401931-chr16:48416758..48423536,12	MCF-7	breast:
26	chr10:35284036..35284536-chr16:48418817..48419320,2	NB4	blood:
27	chr16:48417608..48421302-chr16:48425063..48429266,6	K562	blood:
28	chr11:6502371..6503037-chr16:48419377..48420020,2	NB4	blood:
29	chr16:48417371..48420713-chr16:48642499..48645364,3	K562	blood:
30	chr16:48367808..48369426-chr16:48417936..48419640,2	MCF-7	breast:

Variant related genes	Relation type
SIAH1	TF binding region
ENSG00000240793	chromatin interactions
ENSG00000166716	chromatin interactions
ENSG00000121270	chromatin interactions
ENSG00000255513	chromatin interactions
ENSG00000143493	chromatin interactions
ENSG00000132286	chromatin interactions
ENSG00000130303	chromatin interactions
ENSG00000110955	chromatin interactions
ENSG00000264395	chromatin interactions
ENSG00000102921	chromatin interactions
ENSG00000140988	chromatin interactions
ENSG00000197956	chromatin interactions
ENSG00000167526	chromatin interactions
ENSG00000198911	chromatin interactions
ENSG00000139178	chromatin interactions
ENSG00000196470	chromatin interactions
ENSG00000255198	chromatin interactions
ENSG00000102910	chromatin interactions
ENSG00000143476	chromatin interactions
ENSG00000132254	chromatin interactions
ENSG00000205885	chromatin interactions
ENSG00000265264	chromatin interactions

Extended variants
information (count: 18 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs559634680	chr16:48418565-48418566	Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
2	rs573032808	chr16:48418566-48418567	Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
3	rs111404391	chr16:48418660-48418661	Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
4	rs545466427	chr16:48418824-48418825	Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
5	rs112033176	chr16:48418901-48418902	Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
6	rs191324932	chr16:48418957-48418958	Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a
7	rs565270861	chr16:48419097-48419098	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	16 gene(s)	Overlapped CNVs	n/a
8	rs538295503	chr16:48419123-48419124	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	16 gene(s)	Overlapped CNVs	n/a
9	rs551099380	chr16:48419225-48419226	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	17 gene(s)	Overlapped CNVs	n/a
10	rs561200032	chr16:48419279-48419280	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	17 gene(s)	Overlapped CNVs	n/a
11	rs543688431	chr16:48419292-48419293	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	17 gene(s)	Overlapped CNVs	n/a
12	rs530334391	chr16:48419363-48419364	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
13	rs546859601	chr16:48419394-48419395	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	20 gene(s)	Overlapped CNVs	n/a
14	rs542576035	chr16:48419405-48419406	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	20 gene(s)	Overlapped CNVs	n/a
15	rs567178507	chr16:48419408-48419409	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	20 gene(s)	Overlapped CNVs	n/a
16	rs541337707	chr16:48419425-48419426	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	19 gene(s)	Overlapped CNVs	n/a
17	rs532662132	chr16:48419433-48419434	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	19 gene(s)	Overlapped CNVs	n/a
18	rs551000602	chr16:48419466-48419467	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	19 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Autism	19415332	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Schizophrenia	22958593	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Wilms tumour	21544195	CNVD
Cancer	20164920	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16702952	CNVD
Medulloblastoma	16968546	CNVD
Prostate cancer	19242612	CNVD
Cancer	22429812	CNVD
Ewing''s sarcoma	21437220	CNVD
Ewing''s sarcoma	22429812	CNVD
Melanoma	18172304	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	20837533	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Multiple myeloma	21628407	CNVD
Renal cell carcinoma	18765545	CNVD
Sudden cardiac death	19188705	CNVD
Multiple myeloma	16616336	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	21858162	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Breast cancer	21364760	CNVD
Ewing''s sarcoma	17952124	CNVD
Myelofibrosis	22110671	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Bladder cancer	21909424	CNVD
Colorectal cancer	19359472	CNVD
Olfactory neuroblastoma	18408657	CNVD
Prostate cancer	16461572	CNVD
Breast cancer	17001317	CNVD
Breast cancer	17133270	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Disease	22140031	CNVD
Non-syndromic sensorineural hearing loss	22140031	CNVD
Prostate cancer	22341455	CNVD

Chromatin state (count:149 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48415400-48419800	Active TSS	GM12878-XiMat	blood
2	chr16:48416800-48420200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:48416800-48420200	Active TSS	HSMMtube	muscle
4	chr16:48416800-48420400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr16:48417000-48418600	Active TSS	Fetal Kidney	kidney
6	chr16:48417000-48419800	Active TSS	Brain Germinal Matrix	brain
7	chr16:48417000-48419800	Active TSS	Placenta	Placenta
8	chr16:48417000-48419800	Active TSS	HMEC	breast
9	chr16:48417000-48419800	Active TSS	NHLF	lung
10	chr16:48417000-48420000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr16:48417000-48420000	Active TSS	NHDF-Ad	bronchial
12	chr16:48417200-48418600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr16:48417200-48419000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr16:48417200-48419000	Active TSS	Right Atrium	heart
15	chr16:48417200-48419800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr16:48417200-48419800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:48417200-48419800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:48417200-48419800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:48417200-48420000	Active TSS	Aorta	Aorta
20	chr16:48417200-48420000	Active TSS	Fetal Intestine Large	intestine
21	chr16:48417200-48420000	Active TSS	Ovary	ovary
22	chr16:48417200-48420200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr16:48417200-48420200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr16:48417200-48420200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr16:48417200-48420200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr16:48417200-48420200	Active TSS	Psoas Muscle	Psoas
27	chr16:48417400-48418600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr16:48417400-48418600	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr16:48417400-48419800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr16:48417400-48419800	Active TSS	Colonic Mucosa	Colon
31	chr16:48417400-48419800	Active TSS	Fetal Muscle Leg	muscle
32	chr16:48417400-48419800	Active TSS	Fetal Stomach	stomach
33	chr16:48417400-48419800	Active TSS	Right Ventricle	heart
34	chr16:48417400-48419800	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr16:48417400-48420000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr16:48417400-48420000	Active TSS	Brain Angular Gyrus	brain
37	chr16:48417400-48420000	Active TSS	HSMM	muscle
38	chr16:48417400-48420200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr16:48417400-48420200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr16:48417400-48420200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr16:48417400-48420200	Active TSS	Fetal Brain Female	brain
42	chr16:48417400-48420200	Active TSS	Fetal Intestine Small	intestine
43	chr16:48417600-48418600	Active TSS	Fetal Brain Male	brain
44	chr16:48417600-48419800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr16:48417600-48419800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr16:48417600-48419800	Active TSS	Brain Anterior Caudate	brain
47	chr16:48417600-48419800	Active TSS	Fetal Muscle Trunk	muscle
48	chr16:48417600-48419800	Active TSS	A549	lung
49	chr16:48417600-48420000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr16:48417600-48420000	Active TSS	Brain Hippocampus Middle	brain

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