Variant report

Variant	nsv946007
Chromosome Location	chr1:78313518-78314481
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	FOXM1	chr1:78313303-78313856	GM12878	blood:	n/a	n/a
2	GTF2F1	chr1:78313762-78313766	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFIC	chr1:78313417-78313975	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:78313764-78313799	Hela-S3	cervix:	n/a	n/a
5	RUNX3	chr1:78313340-78313831	GM12878	blood:	n/a	n/a
6	RUNX3	chr1:78313268-78313980	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
HSPE1P25	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs55775281	chr1:78313547-78313548	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs554015362	chr1:78313555-78313556	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs186155379	chr1:78313598-78313599	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs569574583	chr1:78313612-78313613	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs573964045	chr1:78313631-78313632	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs536397831	chr1:78313634-78313635	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs555154391	chr1:78313689-78313690	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs572815181	chr1:78313729-78313730	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs540344399	chr1:78313745-78313746	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs558256714	chr1:78313747-78313748	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs576412652	chr1:78313765-78313766	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs543842497	chr1:78313800-78313801	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs562437548	chr1:78313977-78313978	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs190920264	chr1:78313989-78313990	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs541622281	chr1:78314066-78314067	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs377288367	chr1:78314072-78314073	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560312526	chr1:78314074-78314075	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs6695986	chr1:78314080-78314081	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs146709807	chr1:78314095-78314096	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs565412455	chr1:78314123-78314124	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs139670982	chr1:78314160-78314161	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs550996942	chr1:78314164-78314165	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs7410814	chr1:78314263-78314264	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs536966495	chr1:78314282-78314283	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs144438391	chr1:78314298-78314299	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs534145618	chr1:78314313-78314314	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs567031483	chr1:78314347-78314348	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs146625303	chr1:78314349-78314350	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs558217969	chr1:78314420-78314421	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs576573757	chr1:78314440-78314441	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs369330475	chr1:78314446-78314447	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs537404002	chr1:78314457-78314458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs556136563	chr1:78314465-78314466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs574612759	chr1:78314468-78314469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs12409958	chr1:78314478-78314479	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:102)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	17133270	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Ewing''s sarcoma	17952124	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Poland''s syndrome	22110015	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21922591	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Cancer	22429812	CNVD
Effusion lymphoma	18079361	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Colorectal cancer	16774939	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
2	chr1:78280600-78325600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:78281200-78316400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:78284600-78333000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:78285600-78332000	Weak transcription	Spleen	Spleen
7	chr1:78286400-78333200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:78286600-78328400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:78290200-78334200	Weak transcription	Gastric	stomach
10	chr1:78295200-78318400	Weak transcription	Ovary	ovary
11	chr1:78296800-78329000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:78298400-78340400	Weak transcription	Colonic Mucosa	Colon
13	chr1:78298600-78327000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:78298600-78352400	Weak transcription	Right Ventricle	heart
15	chr1:78298800-78332800	Weak transcription	Fetal Kidney	kidney
16	chr1:78299000-78315400	Weak transcription	Fetal Brain Female	brain
17	chr1:78299200-78314800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:78299400-78340200	Weak transcription	NHEK	skin
19	chr1:78299400-78341200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:78299600-78340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:78299600-78343000	Weak transcription	K562	blood
22	chr1:78299600-78353800	Weak transcription	Brain Substantia Nigra	brain
23	chr1:78300200-78331600	Weak transcription	Lung	lung
24	chr1:78300200-78332600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:78300800-78320600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:78300800-78328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:78300800-78342200	Weak transcription	Fetal Brain Male	brain
28	chr1:78301400-78325600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:78301400-78332800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:78301400-78353200	Weak transcription	HSMMtube	muscle
31	chr1:78301800-78342400	Weak transcription	NHLF	lung
32	chr1:78302000-78332000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:78302200-78315800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:78302800-78334200	Weak transcription	HepG2	liver
35	chr1:78303600-78315800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:78303800-78326000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:78303800-78332800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:78304000-78320600	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:78305800-78316600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:78305800-78319000	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:78305800-78319200	Weak transcription	Brain Anterior Caudate	brain
42	chr1:78305800-78320800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:78305800-78332200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:78305800-78342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:78306000-78342600	Weak transcription	Brain Angular Gyrus	brain
46	chr1:78309200-78328800	Weak transcription	NH-A	brain
47	chr1:78309200-78352400	Weak transcription	Aorta	Aorta
48	chr1:78309400-78320000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:78309400-78324400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:78309400-78324600	Weak transcription	Liver	Liver

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