Variant report

Variant	esv3436377
Chromosome Location	chr1:45963015-45964113
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr1:45963635-45964035	K562	blood:	n/a	n/a
2	SETDB1	chr1:45963009-45963209	U2OS	brain:	n/a	n/a
3	ZNF384	chr1:45964045-45964138	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45963190-45963240	PFSK-1	brain:	n/a
2	chr1:45963190-45963240	Hela-S3	cervix:	n/a
3	chr1:45963190-45963240	HRE	kidney:	n/a
4	chr1:45963190-45963240	GM19239	blood:	n/a
5	chr1:45963190-45963240	AG09309	skin:	n/a
6	chr1:45963190-45963240	A549	lung:	n/a
7	chr1:45963190-45963240	LNCaP	prostate:	n/a
8	chr1:45963190-45963240	IMR90	lung:	fetal
9	chr1:45963190-45963240	U87	brain:	n/a
10	chr1:45963190-45963240	HRCEpiC	kidney:	n/a
11	chr1:45963190-45963240	HIPEpiC	eye:	n/a
12	chr1:45963190-45963240	MCF10A-Er-Src	breast:	n/a
13	chr1:45963190-45963240	K562	blood:	n/a
14	chr1:45963190-45963240	HAEpiC	amniotic membrane:	n/a
15	chr1:45963190-45963240	HUVEC	blood vessel:	n/a
16	chr1:45963190-45963240	SK-N-MC	brain:	n/a
17	chr1:45963190-45963240	GM12892	blood:	n/a
18	chr1:45963190-45963240	HEK293	kidney:	embryo
19	chr1:45963190-45963240	HNPCEpiC	eye:	n/a
20	chr1:45963190-45963240	PANC-1	pancreas:	n/a
21	chr1:45963190-45963240	ovcar-3	ovarian:	n/a
22	chr1:45963190-45963240	SAEC	small airway:	n/a
23	chr1:45963190-45963240	HCF	heart:	n/a
24	chr1:45963190-45963240	PrEC	prostate:	n/a
25	chr1:45963190-45963240	AG04449	skin:	fetal
26	chr1:45963190-45963240	CMK	blood:	n/a
27	chr1:45963190-45963240	SKMC	muscle:	n/a
28	chr1:45963190-45963240	HCPEpiC	choroid plexus:	n/a
29	chr1:45963190-45963240	NB4	blood:	n/a
30	chr1:45963190-45963240	SK-N-SH_RA	brain:	n/a
31	chr1:45963190-45963240	HMEC	breast:	n/a
32	chr1:45963190-45963240	SK-N-SH	brain:	n/a
33	chr1:45963190-45963240	Hepatocyte	liver:	n/a
34	chr1:45963190-45963240	GM12891	blood:	n/a
35	chr1:45963190-45963240	GM12878	blood:	n/a
36	chr1:45963190-45963240	NHBE	bronchial:	n/a
37	chr1:45963190-45963240	NH-A	brain:	n/a
38	chr1:45963190-45963240	Jurkat	blood:	n/a
39	chr1:45963190-45963240	Caco-2	colon:	n/a
40	chr1:45963190-45963240	BJ	skin:	n/a
41	chr1:45963190-45963240	ProgFib	skin:	n/a
42	chr1:45963190-45963240	HepG2	liver:	n/a
43	chr1:45963190-45963240	AoSMC	blood vessel:	n/a
44	chr1:45963190-45963240	HRPEpiC	eye:	n/a
45	chr1:45963190-45963240	GM06990	blood:	n/a
46	chr1:45963190-45963240	AG04450	lung:	fetal
47	chr1:45963190-45963240	NT2-D1	testis:	n/a
48	chr1:45963190-45963240	AG10803	skin:	n/a
49	chr1:45963190-45963240	RPTEC	kidney:	n/a
50	chr1:45963190-45963240	HCM	heart:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
2	chr1:45961218..45963399-chr1:45963495..45965607,2	K562	blood:
3	chr1:45806085..45807923-chr1:45963911..45966246,2	MCF-7	breast:
4	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
5	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
6	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:
7	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
8	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TESK2-1	chr1:45962971-45963060	NONHSAT002942
2	lnc-TESK2-1	chr1:45962971-45963055	NR_033296
3	lnc-TESK2-1	chr1:45962971-45963055	NR_033298
4	lnc-TESK2-1	chr1:45962971-45963055	NONHSAT002941

No data

Variant related genes	Relation type
MMACHC	TF binding region
MMACHC	CpG island
ENSG00000070759	chromatin interactions
ENSG00000236624	chromatin interactions
ENSG00000132773	chromatin interactions
ENSG00000202444	chromatin interactions
ENSG00000132780	chromatin interactions
ENSG00000132781	chromatin interactions

Extended variants
information (count: 61 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:61 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370706411	chr1:45963039-45963040	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	Overlapped CNVs	n/a
2	rs549144434	chr1:45963043-45963044	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	Overlapped CNVs	n/a
3	rs562688214	chr1:45963049-45963050	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	Overlapped CNVs	n/a
4	rs375342737	chr1:45963077-45963078	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs368600093	chr1:45963082-45963083	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs372978623	chr1:45963093-45963094	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs374826534	chr1:45963097-45963098	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs531702092	chr1:45963106-45963107	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs375171236	chr1:45963134-45963135	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs551811249	chr1:45963182-45963183	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs571552459	chr1:45963190-45963191	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs550723584	chr1:45963191-45963192	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs74227021	chr1:45963200-45963201	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs183867951	chr1:45963210-45963211	Weak transcription	CpG island Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs567549524	chr1:45963215-45963216	Weak transcription	CpG island Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs536500924	chr1:45963223-45963224	Weak transcription	CpG island Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs12066142	chr1:45963249-45963250	Weak transcription	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs186097550	chr1:45963332-45963333	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs199639390	chr1:45963342-45963343	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs6671329	chr1:45963347-45963348	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs61788290	chr1:45963351-45963352	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs61788291	chr1:45963355-45963356	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs373024152	chr1:45963360-45963361	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs113041898	chr1:45963381-45963382	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs188605625	chr1:45963409-45963410	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs112100428	chr1:45963417-45963418	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	mRNA abundance
27	rs374833276	chr1:45963434-45963435	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs200718196	chr1:45963458-45963459	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs61788292	chr1:45963463-45963464	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs61788293	chr1:45963466-45963467	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs61788326	chr1:45963471-45963472	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs61788327	chr1:45963478-45963479	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs61788328	chr1:45963480-45963481	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	mRNA abundance
34	rs61788329	chr1:45963482-45963483	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs61788330	chr1:45963490-45963491	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs61788331	chr1:45963495-45963496	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	mRNA abundance
37	rs61788332	chr1:45963501-45963502	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs61788333	chr1:45963508-45963509	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs576148038	chr1:45963525-45963526	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs61788334	chr1:45963527-45963528	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
41	rs190241151	chr1:45963528-45963529	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs369829302	chr1:45963580-45963581	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs538359966	chr1:45963653-45963654	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
44	rs558594339	chr1:45963667-45963668	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
45	rs571962809	chr1:45963704-45963705	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
46	rs541006838	chr1:45963763-45963764	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
47	rs560441404	chr1:45963769-45963770	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
48	rs562599578	chr1:45963796-45963797	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
49	rs567269535	chr1:45963874-45963875	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
50	rs573991437	chr1:45963893-45963894	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

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
Breast cancer	22522925	CNVD
Schizophrenia	20967226	CNVD

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45964600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:45956800-45964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:45956800-45964800	Weak transcription	Spleen	Spleen
4	chr1:45956800-45965000	Weak transcription	Gastric	stomach
5	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
6	chr1:45957000-45964200	Weak transcription	Pancreas	Pancrea
7	chr1:45957000-45964400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:45957000-45964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:45957000-45964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:45957200-45964200	Weak transcription	K562	blood
11	chr1:45957400-45964000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:45957400-45964600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:45957400-45965200	Weak transcription	HSMM	muscle
14	chr1:45957600-45964000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:45957600-45964000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:45957600-45964200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:45957600-45964200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:45957600-45964200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:45957600-45964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:45957600-45964600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:45957600-45964600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:45957600-45964600	Weak transcription	Ovary	ovary
23	chr1:45957600-45964600	Weak transcription	Thymus	Thymus
24	chr1:45957600-45964600	Weak transcription	Osteobl	bone
25	chr1:45957600-45964800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:45957600-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:45957600-45964800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:45957600-45965000	Weak transcription	Psoas Muscle	Psoas
29	chr1:45957800-45964000	Weak transcription	Liver	Liver
30	chr1:45957800-45964000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:45957800-45964000	Weak transcription	Brain Substantia Nigra	brain
32	chr1:45957800-45964200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:45957800-45964400	Weak transcription	Brain Angular Gyrus	brain
34	chr1:45957800-45964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:45957800-45964600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:45957800-45964600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:45957800-45964800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:45957800-45964800	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:45957800-45965000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:45957800-45965000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:45958000-45964000	Weak transcription	Dnd41	blood
42	chr1:45958000-45964200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:45958000-45964200	Weak transcription	GM12878-XiMat	blood
44	chr1:45958000-45964400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:45958000-45964400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:45958000-45964400	Weak transcription	Fetal Thymus	thymus
47	chr1:45958000-45964400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:45958000-45964600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:45958000-45964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:45958000-45964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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