Variant report

Variant	esv3358613
Chromosome Location	chr15:77991892-77992066
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr15:77992014-77992206	GM12878	blood:	n/a	n/a
2	CHD2	chr15:77991748-77992099	GM12878	blood:	n/a	n/a
3	CTCF	chr15:77991923-77992167	GM19239	blood:	n/a	n/a
4	CTCF	chr15:77991960-77992110	WERI-Rb-1	eye:	n/a	n/a
5	CTCF	chr15:77991900-77992050	HRPEpiC	eye:	n/a	n/a
6	CTCF	chr15:77991900-77992050	BE2_C	brain:	n/a	n/a
7	CTCF	chr15:77991940-77992090	GM12872	blood:	n/a	n/a
8	CTCF	chr15:77992000-77992150	GM12869	blood:	n/a	n/a
9	CTCF	chr15:77991844-77991900	GM19239	blood:	n/a	n/a
10	CTCF	chr15:77991940-77992090	AG04449	skin:	n/a	n/a
11	CTCF	chr15:77991940-77992090	GM12873	blood:	n/a	n/a
12	CTCF	chr15:77991924-77992147	MCF-7	breast:	n/a	n/a
13	CTCF	chr15:77991920-77992070	GM12865	blood:	n/a	n/a
14	ELK1	chr15:77991744-77992029	Hela-S3	cervix:	n/a	n/a
15	ELK1	chr15:77991852-77992082	GM12878	blood:	n/a	n/a
16	ESRRA	chr15:77991723-77992185	GM12878	blood:	n/a	n/a
17	GTF2F1	chr15:77991746-77992197	Hela-S3	cervix:	n/a	n/a
18	GTF2F1	chr15:77991587-77992045	K562	blood:	n/a	n/a
19	IRF3	chr15:77991926-77992099	GM12878	blood:	n/a	n/a
20	MAFK	chr15:77991724-77992133	K562	blood:	n/a	n/a
21	MAZ	chr15:77991755-77992212	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr15:77991881-77992131	Hela-S3	cervix:	n/a	n/a
23	MYC	chr15:77991886-77992165	MCF-7	breast:	n/a	n/a
24	MYC	chr15:77991861-77991954	GM12878	blood:	n/a	n/a
25	MYC	chr15:77991940-77992108	HUVEC	blood vessel:	n/a	n/a
26	MYC	chr15:77991857-77992156	MCF-7	breast:	n/a	n/a
27	NR2C2	chr15:77991562-77992263	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:77991950-77992042	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr15:77991698-77991895	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr15:77991996-77992044	Gliobla	brain:	n/a	n/a
31	RCOR1	chr15:77991697-77992146	K562	blood:	n/a	n/a
32	RCOR1	chr15:77991811-77992270	Hela-S3	cervix:	n/a	n/a
33	RFX5	chr15:77991895-77992209	GM12878	blood:	n/a	n/a
34	SUZ12	chr15:77991580-77992275	H1-hESC	embryonic stem cell:	n/a	n/a
35	TBP	chr15:77991751-77991926	K562	blood:	n/a	n/a
36	USF2	chr15:77991763-77992037	K562	blood:	n/a	n/a
37	USF2	chr15:77991731-77991999	Hela-S3	cervix:	n/a	n/a
38	USF2	chr15:77991731-77992095	HepG2	liver:	n/a	n/a
39	ZKSCAN1	chr15:77991744-77992166	Hela-S3	cervix:	n/a	n/a
40	ZNF143	chr15:77991737-77992218	Hela-S3	cervix:	n/a	n/a
41	ZNF263	chr15:77991579-77992664	HEK293-T-REx	kidney:	n/a	chr15:77992297-77992306 chr15:77992112-77992133 chr15:77992546-77992555
42	ZNF274	chr15:77991850-77992079	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77986790..77988605-chr15:77991712..77993681,2	K562	blood:
2	chr15:77979748..77982431-chr15:77989857..77992919,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMG20A-5	chr15:77991916-77991946	XLOC_011316
2	lnc-HMG20A-5	chr15:77992011-77992117	XLOC_011316

No data

Variant related genes	Relation type
LINGO1	TF binding region
ENSG00000169783	chromatin interactions

Extended variants
information (count: 34 )
Associated
traits (count: 51 )

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs76604485	chr15:77991893-77991894	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs531725992	chr15:77991895-77991896	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs59511331	chr15:77991899-77991900	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs550205437	chr15:77991901-77991902	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs67486172	chr15:77991909-77991910	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs564932811	chr15:77991917-77991918	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs532395334	chr15:77991921-77991922	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs62009136	chr15:77991930-77991931	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs79383439	chr15:77991942-77991943	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs547604682	chr15:77991947-77991948	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs57786438	chr15:77991958-77991959	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs57889431	chr15:77991959-77991960	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs57555174	chr15:77991967-77991968	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs62009139	chr15:77991969-77991970	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs7402488	chr15:77991973-77991974	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs7402497	chr15:77991980-77991981	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs62009140	chr15:77991990-77991991	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs61083622	chr15:77991996-77991997	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs566012421	chr15:77991998-77991999	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs536527110	chr15:77992000-77992001	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs61466103	chr15:77992004-77992005	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs60182143	chr15:77992006-77992007	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs62009142	chr15:77992021-77992022	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs58731634	chr15:77992023-77992024	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
25	rs61104393	chr15:77992024-77992025	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
26	rs547894163	chr15:77992027-77992028	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
27	rs57172971	chr15:77992030-77992031	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs61431246	chr15:77992043-77992044	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs76465389	chr15:77992049-77992050	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs373632516	chr15:77992052-77992053	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs368708914	chr15:77992053-77992054	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
32	rs79519843	chr15:77992056-77992057	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
33	rs78897048	chr15:77992057-77992058	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
34	rs59881423	chr15:77992064-77992065	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:51)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Wilms tumour	21544195	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
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
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Cancer	16751803	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	17133270	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	17322880	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Myelofibrosis	22110671	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Papillary thyroid carcinoma	22161024	CNVD
Autism	21480499	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	16864856	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77969200-78007600	Weak transcription	Right Atrium	heart
2	chr15:77991600-77992200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
3	chr15:77991600-77992200	ZNF genes & repeats	Brain Angular Gyrus	brain
4	chr15:77991600-77992200	ZNF genes & repeats	Fetal Brain Male	brain
5	chr15:77991800-77992000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr15:77991800-77992000	Bivalent/Poised TSS	Hela-S3	cervix
7	chr15:77991800-77992200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:77991800-77992200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:77991800-77992200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
10	chr15:77991800-77992200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:77991800-77992200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:77991800-77992200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
13	chr15:77991800-77992200	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr15:77991800-77992200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:77991800-77992200	ZNF genes & repeats	Brain Substantia Nigra	brain
16	chr15:77991800-77992200	ZNF genes & repeats	Colon Smooth Muscle	Colon
17	chr15:77991800-77992200	ZNF genes & repeats	Esophagus	oesophagus
18	chr15:77991800-77992200	ZNF genes & repeats	Fetal Kidney	kidney
19	chr15:77991800-77992200	ZNF genes & repeats	Fetal Lung	lung
20	chr15:77991800-77992200	Bivalent Enhancer	Fetal Stomach	stomach
21	chr15:77991800-77992200	ZNF genes & repeats	Gastric	stomach
22	chr15:77991800-77992200	ZNF genes & repeats	Lung	lung
23	chr15:77991800-77992200	ZNF genes & repeats	Pancreas	Pancrea
24	chr15:77991800-77992200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
25	chr15:77991800-77992200	ZNF genes & repeats	Spleen	Spleen
26	chr15:77991800-77992200	Bivalent/Poised TSS	GM12878-XiMat	blood
27	chr15:77991800-77992200	ZNF genes & repeats	NHLF	lung
28	chr15:77992000-77992200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:77992000-77992200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:77992000-77992200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
31	chr15:77992000-77992200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
32	chr15:77992000-77992200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
33	chr15:77992000-77992200	Bivalent/Poised TSS	Stomach Mucosa	stomach
34	chr15:77992000-77992200	Flanking Bivalent TSS/Enh	Hela-S3	cervix
35	chr15:77992000-77992200	Bivalent/Poised TSS	NHDF-Ad	bronchial

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