Variant report

Variant	esv3311135
Chromosome Location	chr15:41859644-41860466
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr15:41860068-41860472	H1-hESC	embryonic stem cell:	n/a	n/a
2	BRCA1	chr15:41860114-41861134	H1-hESC	embryonic stem cell:	n/a	n/a
3	CCNT2	chr15:41860239-41860243	K562	blood:	n/a	n/a
4	CHD1	chr15:41860335-41860894	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr15:41859986-41860374	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr15:41860215-41860376	HepG2	liver:	n/a	n/a
7	EP300	chr15:41860197-41860384	HepG2	liver:	n/a	n/a
8	FOXA1	chr15:41860431-41861032	HepG2	liver:	n/a	n/a
9	FOXA1	chr15:41860436-41861138	HepG2	liver:	n/a	n/a
10	GTF2F1	chr15:41859932-41861122	H1-hESC	embryonic stem cell:	n/a	n/a
11	HEY1	chr15:41860132-41861071	HepG2	liver:	n/a	n/a
12	HEY1	chr15:41859977-41861129	HepG2	liver:	n/a	n/a
13	HNF4A	chr15:41860136-41860391	HepG2	liver:	n/a	n/a
14	JUND	chr15:41860068-41860278	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr15:41859987-41860346	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr15:41860195-41860205	HepG2	liver:	n/a	n/a
17	MXI1	chr15:41860079-41860366	HepG2	liver:	n/a	n/a
18	NR3C1	chr15:41860133-41860307	A549	lung:	n/a	chr15:41860222-41860235
19	POLR2A	chr15:41860158-41860277	A549	lung:	n/a	n/a
20	POLR2A	chr15:41860349-41860497	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:41859643-41859645	MCF-7	breast:	n/a	n/a
22	POLR2A	chr15:41859841-41859842	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr15:41859366-41861492	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr15:41859950-41861404	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:41860045-41861102	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr15:41860149-41860175	HepG2	liver:	n/a	n/a
27	POLR2A	chr15:41860075-41861242	HepG2	liver:	n/a	n/a
28	POLR2A	chr15:41860152-41860277	K562	blood:	n/a	n/a
29	POLR2A	chr15:41860052-41860378	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr15:41859550-41859879	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr15:41859978-41861269	H1-hESC	embryonic stem cell:	n/a	n/a
32	RCOR1	chr15:41860426-41861219	HepG2	liver:	n/a	n/a
33	RFX5	chr15:41860258-41860410	HepG2	liver:	n/a	n/a
34	RXRA	chr15:41860130-41860450	HepG2	liver:	n/a	n/a
35	SIN3A	chr15:41859944-41861076	H1-hESC	embryonic stem cell:	n/a	n/a
36	SMC3	chr15:41860082-41860408	HepG2	liver:	n/a	n/a
37	SP1	chr15:41859910-41860471	H1-hESC	embryonic stem cell:	n/a	chr15:41860244-41860254 chr15:41860245-41860254
38	SP1	chr15:41860092-41860471	HepG2	liver:	n/a	chr15:41860244-41860254 chr15:41860245-41860254
39	SP1	chr15:41859958-41861183	H1-hESC	embryonic stem cell:	n/a	chr15:41860244-41860254 chr15:41860245-41860254
40	TAF1	chr15:41860095-41860448	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr15:41860084-41861101	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF7	chr15:41860406-41861138	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr15:41860443-41861217	HepG2	liver:	n/a	chr15:41860914-41860923 chr15:41860783-41860792
44	ZBTB7A	chr15:41860346-41861044	HepG2	liver:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41849860..41852803-chr15:41858013..41860929,2	MCF-7	breast:

No data

Variant related genes	Relation type
TYRO3	TF binding region
ENSG00000092445	chromatin interactions

Extended variants
information (count: 37 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200163412	chr15:41859679-41859680	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs267604188	chr15:41859697-41859698	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs55959964	chr15:41859713-41859714	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs144221692	chr15:41859715-41859716	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs202084539	chr15:41859732-41859733	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs145105506	chr15:41859752-41859753	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs189271758	chr15:41859775-41859776	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs376711993	chr15:41859778-41859779	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs368023394	chr15:41859809-41859810	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs146858580	chr15:41859827-41859828	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs568279457	chr15:41859879-41859880	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs576673151	chr15:41859884-41859885	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs545969190	chr15:41859956-41859957	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs562504464	chr15:41859973-41859974	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs4924552	chr15:41859974-41859975	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs375414805	chr15:41859985-41859986	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs140278347	chr15:41859986-41859987	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs527264166	chr15:41860017-41860018	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs547545308	chr15:41860022-41860023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs570561291	chr15:41860026-41860027	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs145320893	chr15:41860069-41860070	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs1200341	chr15:41860073-41860074	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs570120869	chr15:41860144-41860145	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs536160906	chr15:41860194-41860195	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs576442083	chr15:41860210-41860211	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs555768087	chr15:41860241-41860242	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs28657678	chr15:41860270-41860271	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs28622951	chr15:41860273-41860274	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs572134557	chr15:41860284-41860285	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs534693625	chr15:41860305-41860306	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs543503482	chr15:41860325-41860326	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs557871704	chr15:41860334-41860335	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs60774614	chr15:41860364-41860365	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs7171675	chr15:41860411-41860412	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs149022450	chr15:41860425-41860426	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs375950983	chr15:41860446-41860447	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs140010890	chr15:41860450-41860451	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
HDAC8	0	CNVD
NIPBL	0	CNVD
RAD21	0	CNVD
SMC1A	0	CNVD
SMC3	0	CNVD
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Angelman syndrome	16183798	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16774939	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Prostate cancer	16573809	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21785460	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Ovarian cancer	22174824	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	17053054	CNVD
Cancer	20164920	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Cancer	21129771	CNVD
Papillary thyroid carcinoma	22161024	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	21045282	CNVD
Breast cancer	22032731	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelofibrosis	22110671	CNVD
Maculopathy	20981449	CNVD
Gastric adenocarcinoma	19115996	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
2	chr15:41852400-41860600	Weak transcription	HUVEC	blood vessel
3	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:41852600-41877400	Weak transcription	HMEC	breast
5	chr15:41852800-41877400	Weak transcription	NHEK	skin
6	chr15:41853000-41861800	Genic enhancers	Fetal Intestine Large	intestine
7	chr15:41853000-41862000	Genic enhancers	Fetal Intestine Small	intestine
8	chr15:41853200-41860200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:41853200-41861800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:41853200-41863200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
12	chr15:41853400-41859800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
14	chr15:41853600-41859800	Genic enhancers	H1 Cell Line	embryonic stem cell
15	chr15:41853600-41860000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:41853600-41862200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:41853800-41861400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:41853800-41864000	Genic enhancers	Brain Cingulate Gyrus	brain
19	chr15:41854000-41860200	Strong transcription	Dnd41	blood
20	chr15:41854000-41860800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
23	chr15:41855000-41861400	Genic enhancers	Brain Anterior Caudate	brain
24	chr15:41855200-41860000	Weak transcription	Gastric	stomach
25	chr15:41855400-41860200	Weak transcription	Esophagus	oesophagus
26	chr15:41855400-41862000	Weak transcription	NHLF	lung
27	chr15:41855400-41863400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:41855400-41864400	Genic enhancers	Brain Hippocampus Middle	brain
29	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:41855600-41860400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:41855600-41860600	Weak transcription	NH-A	brain
33	chr15:41856200-41860000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:41856400-41861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:41856800-41860400	Weak transcription	Lung	lung
36	chr15:41856800-41861400	Genic enhancers	Brain Angular Gyrus	brain
37	chr15:41857000-41860000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:41857000-41860800	Weak transcription	Brain Germinal Matrix	brain
39	chr15:41857200-41859800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr15:41857200-41860400	Weak transcription	Right Ventricle	heart
41	chr15:41857200-41860800	Weak transcription	HSMMtube	muscle
42	chr15:41857200-41862200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:41857400-41859800	Enhancers	HepG2	liver
44	chr15:41857400-41860400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:41857400-41864000	Genic enhancers	Brain Inferior Temporal Lobe	brain
46	chr15:41857600-41860000	Weak transcription	Placenta	Placenta
47	chr15:41857600-41860200	Weak transcription	Right Atrium	heart
48	chr15:41857600-41863200	Weak transcription	Fetal Brain Female	brain
49	chr15:41858200-41861000	Enhancers	Brain Substantia Nigra	brain
50	chr15:41858200-41861400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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