Variant report

Variant	nsv569528
Chromosome Location	chr15:55654412-55656560
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	chr15:55654793-55654993	HepG2	liver:	n/a	n/a
2	FOXA1	chr15:55654707-55654986	HepG2	liver:	n/a	n/a
3	FOXA1	chr15:55654645-55654974	HepG2	liver:	n/a	n/a
4	FOXA2	chr15:55654698-55654955	HepG2	liver:	n/a	n/a
5	POLR2A	chr15:55654324-55655144	K562	blood:	n/a	n/a
6	POLR2A	chr15:55655520-55656621	K562	blood:	n/a	n/a
7	STAT3	chr15:55656558-55656740	MCF10A-Er-Src	breast:	n/a	n/a
8	ZNF384	chr15:55655951-55655967	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:55622982..55625062-chr15:55652852..55654704,2	MCF-7	breast:
2	chr15:55645555..55647417-chr15:55656372..55659364,2	K562	blood:
3	chr15:55656332..55658633-chr15:55699668..55701557,2	MCF-7	breast:

Variant related genes	Relation type
CCPG1	TF binding region
ENSG00000261652	chromatin interactions
ENSG00000069943	chromatin interactions
ENSG00000260916	chromatin interactions

Extended variants
information (count: 80 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:80 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17819090	chr15:55654412-55654413	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs543251212	chr15:55654471-55654472	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs375417590	chr15:55654504-55654505	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs372122496	chr15:55654525-55654526	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs562832923	chr15:55654530-55654531	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs397942835	chr15:55654537-55654538	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs200277773	chr15:55654539-55654540	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs531881544	chr15:55654582-55654583	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs531352836	chr15:55654623-55654624	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs190747315	chr15:55654682-55654683	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs565315587	chr15:55654691-55654692	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs527697484	chr15:55654707-55654708	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs78640141	chr15:55654745-55654746	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs539366664	chr15:55654775-55654776	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs146014914	chr15:55654779-55654780	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs549205039	chr15:55654906-55654907	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs568835112	chr15:55654939-55654940	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs537976915	chr15:55654958-55654959	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs201120357	chr15:55654994-55654995	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs148269294	chr15:55655011-55655012	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs577684762	chr15:55655022-55655023	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs533772327	chr15:55655049-55655050	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs55706848	chr15:55655057-55655058	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs59891562	chr15:55655062-55655063	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs397797724	chr15:55655066-55655067	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs574426055	chr15:55655100-55655101	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs543241210	chr15:55655107-55655108	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs371673984	chr15:55655108-55655109	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs117798055	chr15:55655122-55655123	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs576443978	chr15:55655185-55655186	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs547737581	chr15:55655195-55655196	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs545450914	chr15:55655208-55655209	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs565259678	chr15:55655250-55655251	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs527634793	chr15:55655271-55655272	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs547399349	chr15:55655315-55655316	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs375797119	chr15:55655333-55655334	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs34939113	chr15:55655334-55655335	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs560010379	chr15:55655338-55655339	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs567595710	chr15:55655363-55655364	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs189970158	chr15:55655367-55655368	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs76237425	chr15:55655379-55655380	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs548886238	chr15:55655404-55655405	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs536633033	chr15:55655451-55655452	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs186020243	chr15:55655464-55655465	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs190542329	chr15:55655520-55655521	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs111265221	chr15:55655532-55655533	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs186654044	chr15:55655534-55655535	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs57094422	chr15:55655553-55655554	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs368574706	chr15:55655562-55655563	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs201531217	chr15:55655566-55655567	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
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
Myelofibrosis	22110671	CNVD
Acute monocytic leukemia	16498392	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Acute lymphoblastic leukemia	21339820	CNVD

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
4	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
5	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
7	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:55623800-55660200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:55630400-55654600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:55630400-55675600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:55630600-55655800	Weak transcription	Brain Angular Gyrus	brain
14	chr15:55630600-55660200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:55630600-55663200	Weak transcription	Fetal Lung	lung
16	chr15:55630600-55667800	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:55630600-55668400	Weak transcription	Brain Substantia Nigra	brain
18	chr15:55630800-55683600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:55631000-55667800	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:55631200-55663200	Weak transcription	Pancreas	Pancrea
21	chr15:55631200-55674000	Weak transcription	Placenta	Placenta
22	chr15:55633600-55667200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:55635800-55675200	Weak transcription	Fetal Brain Male	brain
24	chr15:55636600-55657000	Weak transcription	Fetal Brain Female	brain
25	chr15:55636600-55678200	Weak transcription	Fetal Thymus	thymus
26	chr15:55636800-55666200	Weak transcription	Brain Germinal Matrix	brain
27	chr15:55637000-55660400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:55637000-55663000	Weak transcription	K562	blood
29	chr15:55637000-55663400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:55637000-55671400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:55637400-55680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:55638000-55658200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:55641000-55654800	Weak transcription	HSMMtube	muscle
35	chr15:55641000-55655200	Weak transcription	Lung	lung
36	chr15:55641000-55667800	Weak transcription	Spleen	Spleen
37	chr15:55641000-55668000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:55641000-55671600	Weak transcription	Thymus	Thymus
39	chr15:55641200-55658200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:55641600-55660200	Weak transcription	Gastric	stomach
41	chr15:55643000-55664000	Weak transcription	GM12878-XiMat	blood
42	chr15:55643200-55656400	Weak transcription	Hela-S3	cervix
43	chr15:55644800-55654600	Weak transcription	Brain Anterior Caudate	brain
44	chr15:55645000-55665000	Weak transcription	Fetal Intestine Small	intestine
45	chr15:55645000-55667800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:55645000-55680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:55645200-55657400	Strong transcription	Liver	Liver
48	chr15:55645600-55681400	Weak transcription	Stomach Mucosa	stomach
49	chr15:55646400-55656200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:55646400-55657400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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