Variant report

Variant	nsv945921
Chromosome Location	chr1:46116515-46118136
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:46117240-46117390	GM12865	blood:	n/a	n/a
2	POLR2A	chr1:46117005-46117017	K562	blood:	n/a	n/a
3	POLR2A	chr1:46116300-46117468	K562	blood:	n/a	n/a
4	POLR2A	chr1:46117152-46117166	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:46117237-46117283	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:46117028-46117095	K562	blood:	n/a	n/a
7	POLR2A	chr1:46116233-46117370	K562	blood:	n/a	n/a
8	POLR2A	chr1:46116990-46117004	K562	blood:	n/a	n/a
9	POLR2A	chr1:46116386-46116837	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:46115848-46116937	K562	blood:	n/a	n/a
11	POLR2A	chr1:46117744-46117872	K562	blood:	n/a	n/a
12	POLR2A	chr1:46117104-46117128	K562	blood:	n/a	n/a
13	POLR2A	chr1:46116817-46117512	K562	blood:	n/a	n/a
14	POLR2A	chr1:46116582-46117358	K562	blood:	n/a	n/a
15	POLR2A	chr1:46116572-46116574	GM12878	blood:	n/a	n/a
16	STAT3	chr1:46115860-46116612	MCF10A-Er-Src	breast:	n/a	n/a
17	UBTF	chr1:46117899-46117900	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46113919..46122142-chr1:46149927..46154523,9	K562	blood:
2	chr1:46114955..46116809-chr1:46131648..46134255,2	MCF-7	breast:
3	chr1:46117210..46121553-chr1:46125649..46128637,4	K562	blood:
4	chr1:46115185..46116687-chr1:46151826..46154469,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC17-3	chr1:46116711-46117498	NONHSAT002957

No data

Variant related genes	Relation type
RPS15AP10	TF binding region
ENSG00000234329	TF binding region
ENSG00000159596	chromatin interactions
ENSG00000159592	chromatin interactions

Extended variants
information (count: 53 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:53 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs35962256	chr1:46116720-46116721	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
2	rs12070146	chr1:46116734-46116735	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs12070177	chr1:46116754-46116755	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs188513636	chr1:46116755-46116756	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
5	rs35113723	chr1:46116763-46116764	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
6	rs117807934	chr1:46116777-46116778	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
7	rs192946180	chr1:46116781-46116782	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
8	rs577630823	chr1:46116788-46116789	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
9	rs545059305	chr1:46116808-46116809	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
10	rs373324780	chr1:46116867-46116868	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
11	rs563445112	chr1:46116875-46116876	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs531082554	chr1:46116881-46116882	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs549302709	chr1:46116927-46116928	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
14	rs185499357	chr1:46116959-46116960	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
15	rs528761620	chr1:46116977-46116978	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs547341820	chr1:46116986-46116987	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs565636409	chr1:46116987-46116988	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs150722059	chr1:46117054-46117055	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs569755953	chr1:46117058-46117059	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs537183062	chr1:46117066-46117067	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
21	rs555248142	chr1:46117099-46117100	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs377540411	chr1:46117158-46117159	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs4607935	chr1:46117161-46117162	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs4609469	chr1:46117185-46117186	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs552858841	chr1:46117191-46117192	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
26	rs577569081	chr1:46117238-46117239	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
27	rs376207721	chr1:46117256-46117257	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs544992029	chr1:46117330-46117331	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs139069280	chr1:46117369-46117370	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs575625349	chr1:46117410-46117411	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs142469716	chr1:46117449-46117450	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
32	rs376042064	chr1:46117454-46117455	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
33	rs145979064	chr1:46117465-46117466	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
34	rs12048866	chr1:46117492-46117493	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs374737606	chr1:46117493-46117494	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
36	rs540891754	chr1:46117517-46117518	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs372595194	chr1:46117598-46117599	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs188809045	chr1:46117637-46117638	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs11211153	chr1:46117715-46117716	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs192652057	chr1:46117726-46117727	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs557049132	chr1:46117734-46117735	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs569669680	chr1:46117753-46117754	Strong transcription Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs530490291	chr1:46117790-46117791	Strong transcription Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs554821714	chr1:46117802-46117803	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs568454671	chr1:46117836-46117837	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs534125941	chr1:46117853-46117854	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs549084262	chr1:46117876-46117877	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs567301656	chr1:46117887-46117888	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs534827165	chr1:46117978-46117979	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs554294940	chr1:46118022-46118023	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21080181	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	17603634	CNVD
Soft tissue tumor	16732325	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Adenoid cystic carcinoma	18698036	CNVD
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
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
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
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
Chronic myeloid leukemia	21384125	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	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
Uveal melanoma	20484589	CNVD
Ovarian cancer	22174824	CNVD
Muscle-eye-brain disease	21572526	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	20680643	CNVD
Colorectal cancer	19287155	CNVD
small cell lung cancer	20016488	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Schizophrenia	20967226	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:172 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:46087600-46129200	Strong transcription	Fetal Thymus	thymus
3	chr1:46088600-46127400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:46089600-46126400	Strong transcription	Primary T cells from cord blood	blood
5	chr1:46089800-46127000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:46091000-46126400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr1:46091200-46120400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:46091200-46120800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:46091200-46127000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:46091200-46127000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:46091200-46127200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:46091200-46128200	Strong transcription	Dnd41	blood
13	chr1:46091400-46127000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:46091400-46127000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:46091400-46127000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:46092800-46120200	Strong transcription	HSMM	muscle
17	chr1:46093200-46127000	Strong transcription	K562	blood
18	chr1:46097200-46126800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:46098400-46133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:46100200-46135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:46105400-46116800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:46106200-46140000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:46106400-46120200	Weak transcription	Psoas Muscle	Psoas
24	chr1:46106800-46116800	Weak transcription	Esophagus	oesophagus
25	chr1:46107800-46116800	Weak transcription	Aorta	Aorta
26	chr1:46108200-46116600	Weak transcription	Gastric	stomach
27	chr1:46108200-46116600	Weak transcription	Ovary	ovary
28	chr1:46108200-46116600	Weak transcription	Spleen	Spleen
29	chr1:46108600-46116800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:46108800-46116600	Weak transcription	Colonic Mucosa	Colon
31	chr1:46110600-46120200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:46110600-46122400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:46111200-46120200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr1:46111400-46122200	Strong transcription	GM12878-XiMat	blood
35	chr1:46111400-46126200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:46111400-46126400	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:46111400-46126800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:46111600-46126000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:46112000-46116600	Weak transcription	Pancreas	Pancrea
40	chr1:46112400-46120800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:46112600-46126800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:46112600-46127000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:46112800-46119000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:46112800-46121000	Strong transcription	Fetal Intestine Large	intestine
45	chr1:46112800-46122000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:46112800-46126800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:46113000-46120400	Strong transcription	Osteobl	bone
48	chr1:46113000-46121000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:46113000-46121800	Strong transcription	HepG2	liver
50	chr1:46113000-46126600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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