Variant report

Variant	esv11610
Chromosome Location	chr16:47177258-47178248
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	chr16:47177441-47177480	K562	blood:	n/a	n/a
2	ATF3	chr16:47177260-47177528	K562	blood:	n/a	n/a
3	BACH1	chr16:47176731-47177908	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr16:47178178-47178180	H1-hESC	embryonic stem cell:	n/a	n/a
5	BCLAF1	chr16:47177271-47177669	GM12878	blood:	n/a	chr16:47177425-47177438 chr16:47177593-47177602 chr16:47177563-47177572
6	BCLAF1	chr16:47177145-47177707	GM12878	blood:	n/a	chr16:47177425-47177438 chr16:47177593-47177602 chr16:47177563-47177572
7	BHLHE40	chr16:47177272-47178380	K562	blood:	n/a	chr16:47178152-47178168 chr16:47177449-47177465 chr16:47178004-47178020 chr16:47178144-47178160
8	BHLHE40	chr16:47177335-47177732	HepG2	liver:	n/a	chr16:47177449-47177465
9	BHLHE40	chr16:47176815-47178581	GM12878	blood:	n/a	chr16:47178152-47178168 chr16:47176993-47177009 chr16:47176944-47176960 chr16:47177449-47177465 chr16:47178004-47178020 chr16:47178144-47178160
10	CBX3	chr16:47177298-47177690	K562	blood:	n/a	n/a
11	CCNT2	chr16:47176712-47178516	K562	blood:	n/a	chr16:47177471-47177480
12	CHD1	chr16:47175582-47177806	GM12878	blood:	n/a	n/a
13	CHD1	chr16:47177306-47177565	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD2	chr16:47177362-47178613	Hela-S3	cervix:	n/a	chr16:47178587-47178597 chr16:47177861-47177871
15	CHD2	chr16:47177667-47177736	K562	blood:	n/a	n/a
16	CHD2	chr16:47177538-47177738	HepG2	liver:	n/a	n/a
17	CREB1	chr16:47177189-47177703	K562	blood:	n/a	n/a
18	CREB1	chr16:47177212-47177641	H1-hESC	embryonic stem cell:	n/a	n/a
19	CREB1	chr16:47176829-47177782	HepG2	liver:	n/a	n/a
20	CREB1	chr16:47177138-47178454	A549	lung:	n/a	n/a
21	CTBP2	chr16:47176716-47177734	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTBP2	chr16:47178097-47178658	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr16:47177147-47177916	K562	blood:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
24	CTCF	chr16:47177323-47177562	ECC-1	luminal epithelium:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
25	CTCF	chr16:47177440-47177590	MCF-7	breast:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
26	CTCF	chr16:47178220-47178370	A549	lung:	n/a	n/a
27	CTCF	chr16:47178227-47178478	GM10248	blood:	n/a	n/a
28	CTCF	chr16:47177317-47177648	K562	blood:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
29	CTCF	chr16:47177380-47177530	AG10803	skin:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
30	CTCF	chr16:47177400-47177550	BE2_C	brain:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
31	CTCF	chr16:47177317-47177581	GM13977	blood:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
32	CTCF	chr16:47177400-47177550	AG09319	gingival:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
33	CTCF	chr16:47177325-47177564	MCF-7	breast:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
34	CTCF	chr16:47177300-47177450	HCT-116	colon:	n/a	n/a
35	CTCF	chr16:47177338-47177572	LNCaP	prostate:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
36	CTCF	chr16:47177988-47177994	Fibrobl	skin:	n/a	n/a
37	CTCF	chr16:47178145-47178555	HepG2	liver:	n/a	n/a
38	CTCF	chr16:47177380-47177530	A549	lung:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
39	CTCF	chr16:47177840-47177990	SAEC	small airway:	n/a	n/a
40	CTCF	chr16:47178220-47178495	GM10266	blood:	n/a	n/a
41	CTCF	chr16:47177895-47177897	MCF-7	breast:	n/a	n/a
42	CTCF	chr16:47177420-47177570	NHDF-neo	bronchial:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
43	CTCF	chr16:47177320-47177470	HCM	heart:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
44	CTCF	chr16:47177420-47177570	HRE	kidney:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
45	CTCF	chr16:47177400-47177550	Caco-2	colon:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
46	CTCF	chr16:47177780-47177930	NHEK	skin:	n/a	n/a
47	CTCF	chr16:47177340-47177490	GM12867	blood:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
48	CTCF	chr16:47177210-47177627	A549	lung:	n/a	chr16:47177448-47177461 chr16:47177445-47177463
49	CTCF	chr16:47178203-47178511	MCF-7	breast:	n/a	n/a
50	CTCF	chr16:47177336-47177534	Kidney_OC	kidney:	n/a	chr16:47177448-47177461 chr16:47177445-47177463

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:47178067-47178117	HUVEC	blood vessel:	n/a
2	chr16:47178067-47178117	HUVEC	blood vessel:	n/a
3	chr16:47178067-47178117	PFSK-1	brain:	n/a
4	chr16:47177480-47177530	SK-N-SH_RA	brain:	n/a
5	chr16:47178078-47178128	GM12892	blood:	n/a
6	chr16:47178070-47178120	HPAEpiC	pulmonary alveolar:	n/a
7	chr16:47178208-47178258	Jurkat	blood:	n/a
8	chr16:47178078-47178128	Jurkat	blood:	n/a
9	chr16:47178067-47178117	GM19239	blood:	n/a
10	chr16:47178070-47178120	HEK293	kidney:	embryo
11	chr16:47178070-47178120	NT2-D1	testis:	n/a
12	chr16:47178070-47178120	GM12878	blood:	n/a
13	chr16:47177480-47177530	GM12891	blood:	n/a
14	chr16:47177480-47177530	A549	lung:	n/a
15	chr16:47178070-47178120	MCF-7	breast:	n/a
16	chr16:47178067-47178117	IMR90	lung:	fetal
17	chr16:47178070-47178120	HCPEpiC	choroid plexus:	n/a
18	chr16:47178070-47178120	SK-N-SH_RA	brain:	n/a
19	chr16:47178078-47178128	IMR90	lung:	fetal
20	chr16:47177603-47177653	HCF	heart:	n/a
21	chr16:47178078-47178128	ProgFib	skin:	n/a
22	chr16:47178078-47178128	AG04450	lung:	fetal
23	chr16:47177480-47177530	SK-N-MC	brain:	n/a
24	chr16:47177603-47177653	H1-hESC	embryonic stem cell:	embryo
25	chr16:47177480-47177530	AG09309	skin:	n/a
26	chr16:47177603-47177653	MCF10A-Er-Src	breast:	n/a
27	chr16:47178078-47178128	GM12891	blood:	n/a
28	chr16:47177603-47177653	HCPEpiC	choroid plexus:	n/a
29	chr16:47177480-47177530	NHBE	bronchial:	n/a
30	chr16:47178078-47178128	HepG2	liver:	n/a
31	chr16:47177480-47177530	HRE	kidney:	n/a
32	chr16:47177603-47177653	ovcar-3	ovarian:	n/a
33	chr16:47178208-47178258	HCF	heart:	n/a
34	chr16:47178208-47178258	SKMC	muscle:	n/a
35	chr16:47178208-47178258	HCT-116	colon:	n/a
36	chr16:47178067-47178117	Caco-2	colon:	n/a
37	chr16:47177480-47177530	GM12878	blood:	n/a
38	chr16:47177603-47177653	AG04449	skin:	fetal
39	chr16:47178067-47178117	GM06990	blood:	n/a
40	chr16:47178067-47178117	LNCaP	prostate:	n/a
41	chr16:47177480-47177530	HCT-116	colon:	n/a
42	chr16:47178070-47178120	NB4	blood:	n/a
43	chr16:47178208-47178258	SK-N-MC	brain:	n/a
44	chr16:47177603-47177653	HCT-116	colon:	n/a
45	chr16:47178067-47178117	NH-A	brain:	n/a
46	chr16:47177603-47177653	LNCaP	prostate:	n/a
47	chr16:47177603-47177653	AG09319	gingival:	n/a
48	chr16:47177480-47177530	BJ	skin:	n/a
49	chr16:47178070-47178120	AG04449	skin:	fetal
50	chr16:47178208-47178258	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:47174790..47177797-chr16:47493413..47496816,5	K562	blood:
2	chr16:47175296..47177509-chr16:48190040..48191217,7	MCF-7	breast:
3	chr1:8938804..8939443-chr16:47177378..47177897,2	Hela-S3	cervix:
4	chr16:47177383..47180950-chr16:47184423..47188537,5	K562	blood:
5	chr16:47175994..47177897-chr16:48278487..48280949,2	MCF-7	breast:
6	chr16:47005665..47009288-chr16:47176479..47179650,5	K562	blood:
7	chr16:47175524..47179141-chr16:47493736..47496005,3	MCF-7	breast:
8	chr16:47174837..47177337-chr16:47189035..47191316,2	K562	blood:
9	chr16:47005815..47008447-chr16:47177298..47179122,2	K562	blood:
10	chr16:47176885..47177462-chr16:47479483..47480444,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPT2-3	chr16:47177999-47178405	NONHSAT142282

Variant related genes	Relation type
NETO2	TF binding region
ENSG00000260281	TF binding region
NETO2	CpG island
ENSG00000260281	CpG island
ENSG00000129636	chromatin interactions
ENSG00000102893	chromatin interactions
ENSG00000230679	chromatin interactions
ENSG00000239840	chromatin interactions
ENSG00000069345	chromatin interactions
ENSG00000261173	chromatin interactions
ENSG00000074800	chromatin interactions
ENSG00000121270	chromatin interactions

Extended variants
information (count: 14 )
Associated
traits (count: 63 )

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	rs542633192	chr16:47177259-47177260	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
2	rs560900434	chr16:47177322-47177323	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs139415485	chr16:47177342-47177343	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
4	rs540559113	chr16:47177396-47177397	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
5	rs182520593	chr16:47177402-47177403	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
6	rs532367532	chr16:47177423-47177424	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
7	rs550782687	chr16:47177477-47177478	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
8	rs562589845	chr16:47177524-47177525	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
9	rs529788697	chr16:47177664-47177665	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
10	rs548213305	chr16:47177691-47177692	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
11	rs566424353	chr16:47177801-47177802	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
12	rs533545744	chr16:47177837-47177838	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
13	rs547299759	chr16:47178024-47178025	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
14	rs187168252	chr16:47178246-47178247	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

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
Prostate cancer	22341455	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:195 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47174200-47178400	Active TSS	GM12878-XiMat	blood
2	chr16:47174600-47178800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:47174600-47178800	Active TSS	Fetal Brain Female	brain
4	chr16:47174800-47178400	Active TSS	Brain Germinal Matrix	brain
5	chr16:47175000-47178200	Active TSS	HMEC	breast
6	chr16:47175000-47178800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr16:47175200-47178600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:47175400-47178400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:47175400-47178400	Active TSS	Brain Anterior Caudate	brain
10	chr16:47175400-47178400	Active TSS	NH-A	brain
11	chr16:47175400-47178600	Active TSS	Muscle Satellite Cultured Cells	--
12	chr16:47175400-47178600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr16:47175400-47179000	Active TSS	A549	lung
14	chr16:47175600-47177800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr16:47175600-47178200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr16:47175600-47178200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:47175600-47178200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr16:47175600-47178400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:47175600-47178400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr16:47175600-47178400	Active TSS	Brain Cingulate Gyrus	brain
21	chr16:47175600-47178400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr16:47175600-47178400	Active TSS	Brain Substantia Nigra	brain
23	chr16:47175600-47178400	Active TSS	Ovary	ovary
24	chr16:47175600-47178600	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr16:47175600-47178600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr16:47175600-47178600	Active TSS	NHEK	skin
27	chr16:47175600-47178600	Active TSS	NHLF	lung
28	chr16:47175600-47178600	Active TSS	Osteobl	bone
29	chr16:47175600-47178800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr16:47175600-47178800	Active TSS	Brain Hippocampus Middle	brain
31	chr16:47175600-47179000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:47175600-47179000	Active TSS	Brain Angular Gyrus	brain
33	chr16:47175800-47177400	Active TSS	Right Ventricle	heart
34	chr16:47175800-47177600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr16:47175800-47177600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr16:47175800-47177600	Active TSS	Right Atrium	heart
37	chr16:47175800-47177800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr16:47175800-47178400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr16:47175800-47178400	Active TSS	Aorta	Aorta
40	chr16:47175800-47178400	Active TSS	Left Ventricle	heart
41	chr16:47175800-47178400	Active TSS	NHDF-Ad	bronchial
42	chr16:47175800-47178600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:47175800-47178600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr16:47175800-47178800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr16:47175800-47178800	Active TSS	HSMMtube	muscle
46	chr16:47175800-47179000	Active TSS	Hela-S3	cervix
47	chr16:47176000-47177400	Active TSS	Primary monocytes fromperipheralblood	blood
48	chr16:47176000-47177400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
49	chr16:47176000-47178200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr16:47176000-47178800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

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