Variant report

Variant	esv3412125
Chromosome Location	chr15:52404008-52404454
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr15:52404229-52404244	GM12878	blood:	n/a	n/a
2	CHD2	chr15:52404389-52404825	GM12878	blood:	n/a	n/a
3	CTCF	chr15:52403860-52404010	GM12871	blood:	n/a	n/a
4	CTCF	chr15:52403880-52404030	GM12874	blood:	n/a	n/a
5	CTCF	chr15:52404360-52404510	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr15:52404260-52404410	GM12867	blood:	n/a	n/a
7	CTCF	chr15:52404420-52404570	GM12866	blood:	n/a	n/a
8	CTCF	chr15:52404440-52404590	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr15:52404400-52404550	GM12874	blood:	n/a	n/a
10	CTCF	chr15:52404360-52404510	GM12873	blood:	n/a	n/a
11	CTCF	chr15:52404420-52404570	MCF-7	breast:	n/a	n/a
12	CTCF	chr15:52404360-52404510	HMEC	breast:	n/a	n/a
13	CTCF	chr15:52404400-52404550	AG04449	skin:	n/a	n/a
14	CTCF	chr15:52404320-52404470	GM12874	blood:	n/a	n/a
15	CTCF	chr15:52404420-52404570	BJ	skin:	n/a	n/a
16	CTCF	chr15:52404380-52404530	GM12872	blood:	n/a	n/a
17	CTCF	chr15:52404360-52404510	GM12865	blood:	n/a	n/a
18	CTCF	chr15:52404380-52404530	SAEC	small airway:	n/a	n/a
19	CTCF	chr15:52404280-52404570	GM12871	blood:	n/a	n/a
20	CTCF	chr15:52404380-52404530	HEEpiC	esophagus:	n/a	n/a
21	E2F4	chr15:52404148-52404298	GM12878	blood:	n/a	n/a
22	E2F6	chr15:52404006-52405001	H1-hESC	embryonic stem cell:	n/a	chr15:52404011-52404018 chr15:52404974-52404983
23	E2F6	chr15:52404214-52404897	H1-hESC	embryonic stem cell:	n/a	n/a
24	EBF1	chr15:52404136-52404655	GM12878	blood:	n/a	n/a
25	ELF1	chr15:52403663-52404665	GM12878	blood:	n/a	n/a
26	MAX	chr15:52404100-52404834	MCF-7	breast:	n/a	n/a
27	MAX	chr15:52404255-52404872	GM12878	blood:	n/a	n/a
28	MAX	chr15:52404172-52404728	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr15:52404148-52404873	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr15:52404201-52404300	NB4	blood:	n/a	n/a
31	MAX	chr15:52404172-52404998	MCF-7	breast:	n/a	n/a
32	MAX	chr15:52404245-52404590	H1-hESC	embryonic stem cell:	n/a	n/a
33	MTA3	chr15:52403416-52404901	GM12878	blood:	n/a	n/a
34	MXI1	chr15:52404401-52404634	GM12878	blood:	n/a	n/a
35	MYC	chr15:52404351-52404400	HUVEC	blood vessel:	n/a	n/a
36	MYC	chr15:52404406-52404482	HUVEC	blood vessel:	n/a	n/a
37	MYC	chr15:52404335-52404636	MCF-7	breast:	n/a	n/a
38	MYC	chr15:52403861-52404544	NB4	blood:	n/a	n/a
39	PAX5	chr15:52404292-52404589	GM12892	blood:	n/a	n/a
40	PML	chr15:52403631-52404813	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:52404374-52404380	MCF-7	breast:	n/a	n/a
42	POLR2A	chr15:52403681-52404911	GM12891	blood:	n/a	n/a
43	POLR2A	chr15:52403762-52405802	NB4	blood:	n/a	n/a
44	POLR2A	chr15:52403797-52404959	GM12891	blood:	n/a	n/a
45	POLR2A	chr15:52404242-52404968	GM12878	blood:	n/a	n/a
46	POLR2A	chr15:52403715-52405006	GM19193	blood:	n/a	n/a
47	POLR2A	chr15:52404206-52404973	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:52404381-52404803	MCF-7	breast:	n/a	n/a
49	POLR2A	chr15:52404092-52404988	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:52403812-52404027	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:52404232-52404282	T-47D	breast:	n/a
2	chr15:52404029-52404079	SK-N-SH_RA	brain:	n/a
3	chr15:52404232-52404282	HCPEpiC	choroid plexus:	n/a
4	chr15:52404232-52404282	GM12892	blood:	n/a
5	chr15:52404029-52404079	ProgFib	skin:	n/a
6	chr15:52404029-52404079	HepG2	liver:	n/a
7	chr15:52404029-52404079	HEK293	kidney:	embryo
8	chr15:52404232-52404282	A549	lung:	n/a
9	chr15:52404029-52404079	GM12892	blood:	n/a
10	chr15:52404232-52404282	NH-A	brain:	n/a
11	chr15:52404232-52404282	RPTEC	kidney:	n/a
12	chr15:52404029-52404079	GM12891	blood:	n/a
13	chr15:52404029-52404079	BE2_C	brain:	n/a
14	chr15:52404232-52404282	Caco-2	colon:	n/a
15	chr15:52404029-52404079	NHBE	bronchial:	n/a
16	chr15:52404232-52404282	AG10803	skin:	n/a
17	chr15:52404029-52404079	HEEpiC	esophagus:	n/a
18	chr15:52404029-52404079	HMEC	breast:	n/a
19	chr15:52404029-52404079	AoSMC	blood vessel:	n/a
20	chr15:52404029-52404079	HRPEpiC	eye:	n/a
21	chr15:52404232-52404282	ProgFib	skin:	n/a
22	chr15:52404232-52404282	HAEpiC	amniotic membrane:	n/a
23	chr15:52404029-52404079	AG09309	skin:	n/a
24	chr15:52404232-52404282	HUVEC	blood vessel:	n/a
25	chr15:52404029-52404079	A549	lung:	n/a
26	chr15:52404029-52404079	RPTEC	kidney:	n/a
27	chr15:52404232-52404282	GM12891	blood:	n/a
28	chr15:52404029-52404079	AG04449	skin:	fetal
29	chr15:52404029-52404079	HCT-116	colon:	n/a
30	chr15:52404029-52404079	NT2-D1	testis:	n/a
31	chr15:52404232-52404282	AG09319	gingival:	n/a
32	chr15:52404029-52404079	NB4	blood:	n/a
33	chr15:52404232-52404282	SAEC	small airway:	n/a
34	chr15:52404029-52404079	HNPCEpiC	eye:	n/a
35	chr15:52404029-52404079	SKMC	muscle:	n/a
36	chr15:52404029-52404079	CMK	blood:	n/a
37	chr15:52404029-52404079	ECC-1	luminal epithelium:	n/a
38	chr15:52404232-52404282	HNPCEpiC	eye:	n/a
39	chr15:52404029-52404079	HCM	heart:	n/a
40	chr15:52404232-52404282	GM19239	blood:	n/a
41	chr15:52404029-52404079	MCF-7	breast:	n/a
42	chr15:52404029-52404079	GM19239	blood:	n/a
43	chr15:52404029-52404079	ovcar-3	ovarian:	n/a
44	chr15:52404029-52404079	SAEC	small airway:	n/a
45	chr15:52404232-52404282	Hela-S3	cervix:	n/a
46	chr15:52404232-52404282	HCM	heart:	n/a
47	chr15:52404232-52404282	IMR90	lung:	fetal
48	chr15:52404029-52404079	HCPEpiC	choroid plexus:	n/a
49	chr15:52404232-52404282	Jurkat	blood:	n/a
50	chr15:52404029-52404079	HRCEpiC	kidney:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52263208..52265625-chr15:52404085..52407650,4	MCF-7	breast:
2	chr15:52403961..52406655-chr15:52470750..52472609,2	MCF-7	breast:
3	chr15:52393212..52395889-chr15:52402587..52404691,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259327	TF binding region
ENSG00000259327	CpG island
ENSG00000259577	chromatin interactions
ENSG00000166477	chromatin interactions
ENSG00000069966	chromatin interactions

Extended variants
information (count: 13 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs571624435	chr15:52404027-52404028	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs552002086	chr15:52404051-52404052	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs566759411	chr15:52404100-52404101	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs527652887	chr15:52404109-52404110	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs147876998	chr15:52404163-52404164	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs191789288	chr15:52404168-52404169	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs386783968	chr15:52404215-52404216	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs3751601	chr15:52404216-52404217	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs141397607	chr15:52404243-52404244	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs547588185	chr15:52404256-52404257	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs538560729	chr15:52404270-52404271	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs553994556	chr15:52404309-52404310	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs150387437	chr15:52404398-52404399	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	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
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17053054	CNVD
Breast cancer	22032731	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Cancer	21129771	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Abnormal phenotypes	18644119	CNVD
Cancer	16751803	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Myelofibrosis	22110671	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD

Chromatin state (count:174 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52398600-52404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:52401000-52404200	Enhancers	Primary B cells from peripheral blood	blood
3	chr15:52402200-52404200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:52402200-52404200	Weak transcription	Pancreas	Pancrea
5	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52402400-52405600	Weak transcription	HepG2	liver
7	chr15:52403600-52404200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:52403600-52404200	Weak transcription	HMEC	breast
9	chr15:52403600-52404800	Flanking Active TSS	GM12878-XiMat	blood
10	chr15:52403800-52404200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr15:52403800-52404200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr15:52403800-52404200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:52403800-52404200	Bivalent Enhancer	Fetal Brain Female	brain
14	chr15:52403800-52404400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:52403800-52404400	Bivalent Enhancer	Fetal Intestine Small	intestine
16	chr15:52404000-52404200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:52404000-52404200	Bivalent Enhancer	Primary B cells from cord blood	blood
18	chr15:52404000-52404200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
19	chr15:52404000-52404200	Enhancers	Primary hematopoietic stem cells	blood
20	chr15:52404000-52404200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
21	chr15:52404000-52404200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:52404000-52404200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr15:52404000-52404200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
24	chr15:52404000-52404200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:52404000-52404200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:52404000-52404200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:52404000-52404200	Bivalent Enhancer	Adipose Nuclei	Adipose
28	chr15:52404000-52404200	Bivalent Enhancer	Brain Germinal Matrix	brain
29	chr15:52404000-52404200	Active TSS	Duodenum Mucosa	Duodenum
30	chr15:52404000-52404200	Bivalent Enhancer	Fetal Intestine Large	intestine
31	chr15:52404000-52404200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr15:52404000-52404200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr15:52404000-52404200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
34	chr15:52404000-52404200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
35	chr15:52404000-52404200	Bivalent Enhancer	Osteobl	bone
36	chr15:52404000-52404400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:52404000-52404400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr15:52404000-52404400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr15:52404000-52404400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:52404000-52404400	Enhancers	Liver	Liver
41	chr15:52404000-52404400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr15:52404000-52404400	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chr15:52404000-52404400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
44	chr15:52404000-52404400	Enhancers	Right Ventricle	heart
45	chr15:52404000-52404400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr15:52404000-52404600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:52404000-52404600	Flanking Active TSS	Colonic Mucosa	Colon
48	chr15:52404000-52405000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr15:52404000-52405000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr15:52404000-52405000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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