Variant report

Variant	nsv542521
Chromosome Location	chr15:99869631-99924685
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	chr15:99901786-99902089	HepG2	liver:	n/a	n/a
2	ARID3A	chr15:99880457-99880856	HepG2	liver:	n/a	chr15:99880645-99880661
3	ARID3A	chr15:99883375-99883659	HepG2	liver:	n/a	n/a
4	ARID3A	chr15:99901823-99902129	K562	blood:	n/a	n/a
5	ATF2	chr15:99911569-99912248	GM12878	blood:	n/a	n/a
6	BATF	chr15:99888678-99888879	GM12878	blood:	n/a	n/a
7	BATF	chr15:99911466-99912033	GM12878	blood:	n/a	n/a
8	BATF	chr15:99888611-99888876	GM12878	blood:	n/a	n/a
9	BATF	chr15:99911635-99911973	GM12878	blood:	n/a	n/a
10	BCLAF1	chr15:99905399-99905913	GM12878	blood:	n/a	n/a
11	BCLAF1	chr15:99911540-99912117	GM12878	blood:	n/a	n/a
12	BHLHE40	chr15:99884108-99884275	HepG2	liver:	n/a	n/a
13	BHLHE40	chr15:99905490-99905751	GM12878	blood:	n/a	n/a
14	BHLHE40	chr15:99880229-99880429	K562	blood:	n/a	n/a
15	CEBPB	chr15:99908119-99908476	A549	lung:	n/a	chr15:99908289-99908300
16	CEBPB	chr15:99880990-99881352	IMR90	lung:	n/a	n/a
17	CEBPB	chr15:99908129-99908469	HepG2	liver:	n/a	chr15:99908289-99908300
18	CEBPB	chr15:99908247-99908344	H1-hESC	embryonic stem cell:	n/a	chr15:99908289-99908300
19	CEBPB	chr15:99901718-99902063	IMR90	lung:	n/a	chr15:99901898-99901909
20	CEBPB	chr15:99870103-99870253	K562	blood:	n/a	n/a
21	CEBPB	chr15:99901778-99901979	HepG2	liver:	n/a	chr15:99901898-99901909
22	CEBPB	chr15:99901798-99902017	A549	lung:	n/a	chr15:99901898-99901909
23	CEBPB	chr15:99908141-99908445	IMR90	lung:	n/a	chr15:99908289-99908300
24	CHD2	chr15:99905514-99905714	GM12878	blood:	n/a	n/a
25	CTCF	chr15:99901868-99902096	Medullo	brain:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
26	CTCF	chr15:99884140-99884290	SAEC	small airway:	n/a	n/a
27	CTCF	chr15:99901909-99902051	GM13977	blood:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
28	CTCF	chr15:99901840-99901990	HMEC	breast:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
29	CTCF	chr15:99885008-99885120	GM12878	blood:	n/a	n/a
30	CTCF	chr15:99884040-99884190	HA-sp	spinal cord:	n/a	n/a
31	CTCF	chr15:99884000-99884150	HAc	cerebellar:	n/a	n/a
32	CTCF	chr15:99884060-99884210	MCF-7	breast:	n/a	n/a
33	CTCF	chr15:99911800-99911950	GM12878	blood:	n/a	n/a
34	CTCF	chr15:99884168-99884265	GM10248	blood:	n/a	n/a
35	CTCF	chr15:99901955-99902050	NHEK	skin:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
36	CTCF	chr15:99911840-99911990	GM12873	blood:	n/a	n/a
37	CTCF	chr15:99884108-99884318	Fibrobl	skin:	n/a	n/a
38	CTCF	chr15:99911683-99912024	A549	lung:	n/a	n/a
39	CTCF	chr15:99901821-99902132	HepG2	liver:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
40	CTCF	chr15:99884898-99885244	GM12878	blood:	n/a	n/a
41	CTCF	chr15:99884135-99884311	K562	blood:	n/a	n/a
42	CTCF	chr15:99901703-99902150	A549	lung:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
43	CTCF	chr15:99901920-99902070	AG04450	lung:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
44	CTCF	chr15:99884140-99884290	AG04449	skin:	n/a	n/a
45	CTCF	chr15:99901780-99902145	H1-hESC	embryonic stem cell:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
46	CTCF	chr15:99884120-99884270	HFF-Myc	foreskin:	n/a	n/a
47	CTCF	chr15:99901860-99902010	GM12867	blood:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
48	CTCF	chr15:99901920-99902070	HCPEpiC	choroid plexus:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
49	CTCF	chr15:99901901-99902038	Lung_OC	lung:	n/a	chr15:99901958-99901979 chr15:99901963-99901981
50	CTCF	chr15:99884160-99884310	GM12869	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:99875104..99877834-chr15:99882696..99885261,2	K562	blood:
2	chr15:99896224..99898359-chr15:100106630..100108911,2	MCF-7	breast:
3	chr15:99826430..99827156-chr15:99911339..99912207,2	MCF-7	breast:
4	chr15:99883235..99885875-chr15:99888389..99889955,2	K562	blood:
5	chr15:99889586..99891460-chr15:99894406..99897341,2	K562	blood:
6	chr15:99889586..99891460-chr15:99894406..99897341,2	K562	blood:
7	chr15:99875104..99877834-chr15:99882696..99885261,2	K562	blood:
8	chr15:99826671..99827304-chr15:99901512..99902193,3	MCF-7	breast:
9	chr15:99883235..99885875-chr15:99888389..99889955,2	K562	blood:
10	chr15:99911513..99912231-chr15:100295759..100296289,2	MCF-7	breast:
11	chr15:99892876..99894985-chr15:99896171..99899011,2	K562	blood:
12	chr15:99856565..99859133-chr15:99884132..99886600,2	MCF-7	breast:
13	chr15:99882409..99885385-chr15:99887042..99889200,2	MCF-7	breast:
14	chr15:99909577..99912382-chr15:99924265..99925910,2	MCF-7	breast:
15	chr15:99908481..99910552-chr15:99914998..99917722,2	MCF-7	breast:
16	chr15:99908481..99910552-chr15:99914998..99917722,2	MCF-7	breast:
17	chr15:99900193..99901836-chr15:100106225..100109193,2	MCF-7	breast:
18	chr15:99892876..99894985-chr15:99896171..99899011,2	K562	blood:
19	chr15:99884303..99885875-chr15:99888389..99890129,2	K562	blood:
20	chr15:99883899..99884477-chr15:100244392..100244959,2	MCF-7	breast:
21	chr15:99884303..99885875-chr15:99888389..99890129,2	K562	blood:
22	chr15:99882409..99885385-chr15:99887042..99889200,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MEF2A-6	chr15:99878062-99878686	NONHSAT050865

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	LRRC28	hsa-miR-34a-5p	chr15:99903350-99903371
2	LRRC28	hsa-miR-34a-5p	chr15:99874260-99874282

Variant related genes	Relation type
LRRC28	TF binding region
ENSG00000259257	TF binding region
ENSG00000068305	chromatin interactions
ENSG00000168904	chromatin interactions

Extended variants
information (count: 2173 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:2173 , 50 per page) page: 1 2 3 4 5 6 7 ... 44

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs532772682	chr15:99869679-99869680	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs184052148	chr15:99869697-99869698	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs571798315	chr15:99869721-99869722	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs566410156	chr15:99869786-99869787	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs189414205	chr15:99869810-99869811	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs548136489	chr15:99869868-99869869	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs8034659	chr15:99869900-99869901	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs180911356	chr15:99869905-99869906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs550759813	chr15:99869960-99869961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs185945432	chr15:99869967-99869968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs12591991	chr15:99869968-99869969	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs536443141	chr15:99870014-99870015	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs140388574	chr15:99870035-99870036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs144112523	chr15:99870053-99870054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs76522936	chr15:99870062-99870063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs560838164	chr15:99870073-99870074	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs192483251	chr15:99870130-99870131	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs548856893	chr15:99870148-99870149	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs558074335	chr15:99870157-99870158	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs565029917	chr15:99870173-99870174	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs532593484	chr15:99870203-99870204	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs566740081	chr15:99870273-99870274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs547923241	chr15:99870310-99870311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs144986287	chr15:99870311-99870312	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs530293909	chr15:99870319-99870320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs569961643	chr15:99870376-99870377	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs181889006	chr15:99870508-99870509	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs116018967	chr15:99870607-99870608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs537081544	chr15:99870609-99870610	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs552381517	chr15:99870697-99870698	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs186210636	chr15:99870703-99870704	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs149168741	chr15:99870711-99870712	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs12592717	chr15:99870724-99870725	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs372377018	chr15:99870749-99870750	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs190731091	chr15:99870852-99870853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs182878889	chr15:99870865-99870866	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs554934860	chr15:99870866-99870867	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs576095316	chr15:99870869-99870870	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs543486891	chr15:99870963-99870964	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs543864648	chr15:99870968-99870969	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs536746479	chr15:99870987-99870988	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs552328842	chr15:99870992-99870993	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs566037996	chr15:99871045-99871046	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs113992072	chr15:99871083-99871084	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs12917176	chr15:99871161-99871162	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs559867586	chr15:99871193-99871194	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs530260827	chr15:99871197-99871198	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs542102516	chr15:99871199-99871200	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs73473399	chr15:99871236-99871237	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs191158697	chr15:99871251-99871252	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:67)

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
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
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Cancer	16751803	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	16864856	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
small cell lung cancer	20016488	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Sudden cardiac death	19188705	CNVD
Intellectual disability	22102821	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Developmental delay	21147756	CNVD
Hepatocellular carcinoma	16750200	CNVD
Central neurocytomas	17123091	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Burkitt''s lymphoma	19759907	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	20811773	CNVD
Glioblastoma multiforme	22286061	CNVD
Breast cancer	21364760	CNVD
Breast cancer	20409316	CNVD
Emphysema	19352772	CNVD
Pilocytic astrocytoma	18622384	CNVD
Pilomyxoid astrocytoma	18622384	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	17142309	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:777 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
2	chr15:99847400-99877200	Weak transcription	Ovary	ovary
3	chr15:99853000-99876000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:99853200-99875400	Weak transcription	Fetal Thymus	thymus
5	chr15:99853600-99875800	Weak transcription	Fetal Intestine Large	intestine
6	chr15:99854400-99876000	Weak transcription	Dnd41	blood
7	chr15:99858600-99876600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:99859400-99906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:99861800-99876600	Weak transcription	Primary T cells from cord blood	blood
10	chr15:99863200-99881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:99863200-99899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:99864400-99902200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:99864600-99877200	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:99864800-99881400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:99864800-99884200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr15:99865200-99870800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:99865200-99875800	Weak transcription	Adipose Nuclei	Adipose
18	chr15:99865200-99880600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:99865400-99870800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:99866800-99871600	Weak transcription	HSMMtube	muscle
21	chr15:99866800-99875600	Weak transcription	Left Ventricle	heart
22	chr15:99866800-99875800	Weak transcription	Pancreas	Pancrea
23	chr15:99866800-99877400	Weak transcription	Right Ventricle	heart
24	chr15:99866800-99877800	Weak transcription	Psoas Muscle	Psoas
25	chr15:99866800-99881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:99866800-99882400	Weak transcription	Gastric	stomach
27	chr15:99867000-99871200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:99867000-99880600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:99867200-99869800	Enhancers	A549	lung
30	chr15:99867200-99877400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:99867200-99926600	Weak transcription	NHEK	skin
32	chr15:99868600-99875800	Weak transcription	Liver	Liver
33	chr15:99869000-99877200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:99869200-99870800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:99869200-99880200	Weak transcription	HepG2	liver
36	chr15:99869200-99882000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:99869600-99869800	Enhancers	GM12878-XiMat	blood
38	chr15:99869600-99893400	Weak transcription	Aorta	Aorta
39	chr15:99869800-99870600	Weak transcription	A549	lung
40	chr15:99869800-99884600	Weak transcription	GM12878-XiMat	blood
41	chr15:99870200-99884400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr15:99870200-99884600	Weak transcription	Primary B cells from cord blood	blood
43	chr15:99870600-99870800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr15:99870600-99871400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:99870600-99871600	Enhancers	A549	lung
46	chr15:99870800-99871000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr15:99870800-99871200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:99870800-99871200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:99870800-99871800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr15:99870800-99877000	Weak transcription	Rectal Mucosa Donor 29	rectum

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