Variant report

Variant	nsv947264
Chromosome Location	chr1:62146171-62151947
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	CTCF	chr1:62150529-62150601	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:62150549-62150575	HepG2	liver:	n/a	n/a
3	CTCF	chr1:62150625-62150627	LNCaP	prostate:	n/a	n/a
4	CTCF	chr1:62150539-62150602	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:62150545-62150613	MCF-7	breast:	n/a	n/a
6	CTCF	chr1:62150579-62150610	HepG2	liver:	n/a	n/a
7	CTCF	chr1:62150538-62150620	LNCaP	prostate:	n/a	n/a
8	CTCF	chr1:62147800-62147950	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:62150542-62150603	MCF-7	breast:	n/a	n/a
10	CTCF	chr1:62150547-62150626	GM20000	blood:	n/a	n/a
11	E2F4	chr1:62146261-62146338	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr1:62146235-62146563	MCF10A-Er-Src	breast:	n/a	chr1:62146380-62146388 chr1:62146379-62146389 chr1:62146378-62146390
13	FOS	chr1:62146236-62146564	MCF10A-Er-Src	breast:	n/a	chr1:62146380-62146388 chr1:62146379-62146389 chr1:62146378-62146390
14	FOS	chr1:62146228-62146515	MCF10A-Er-Src	breast:	n/a	chr1:62146380-62146388 chr1:62146379-62146389 chr1:62146378-62146390
15	MAFF	chr1:62146312-62146518	K562	blood:	n/a	chr1:62146377-62146391
16	MAFK	chr1:62146274-62146468	K562	blood:	n/a	chr1:62146374-62146394 chr1:62146377-62146391 chr1:62146376-62146392 chr1:62146381-62146390
17	NFYA	chr1:62147095-62147274	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:62146102-62146360	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:62146987-62147187	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr1:62150642-62150658	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:62150511-62150566	K562	blood:	n/a	n/a
22	POLR2A	chr1:62150573-62150619	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:62146057-62146706	K562	blood:	n/a	n/a
24	POLR2A	chr1:62151067-62151551	K562	blood:	n/a	n/a
25	POLR2A	chr1:62146761-62146847	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr1:62150596-62150639	K562	blood:	n/a	n/a
27	STAT3	chr1:62149634-62149658	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:62136630..62139811-chr1:62142611..62146521,3	K562	blood:
2	chr1:62149064..62151297-chr1:62189288..62192078,2	K562	blood:
3	chr1:62149581..62151297-chr1:62188336..62190788,2	K562	blood:
4	chr1:62151673..62154545-chr1:62190417..62192026,2	K562	blood:
5	chr1:61273051..61275172-chr1:62146602..62149246,2	K562	blood:
6	chr1:62148615..62150124-chr1:62189264..62192017,2	MCF-7	breast:

Variant related genes	Relation type
TM2D1	TF binding region
ENSG00000162604	chromatin interactions

Extended variants
information (count: 206 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:206 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs116095234	chr1:62146186-62146187	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs185412589	chr1:62146219-62146220	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs536229346	chr1:62146239-62146240	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs35215876	chr1:62146246-62146247	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs554674849	chr1:62146258-62146259	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs573107186	chr1:62146260-62146261	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs569125700	chr1:62146369-62146370	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs189422371	chr1:62146370-62146371	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs555897220	chr1:62146384-62146385	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs11207808	chr1:62146438-62146439	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs545254391	chr1:62146512-62146513	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs148026210	chr1:62146522-62146523	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs548138108	chr1:62146545-62146546	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs572036073	chr1:62146575-62146576	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs141741768	chr1:62146602-62146603	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs373539737	chr1:62146631-62146632	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs75844559	chr1:62146649-62146650	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs550405955	chr1:62146658-62146659	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs147200954	chr1:62146662-62146663	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs532713785	chr1:62146746-62146747	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs41289420	chr1:62146778-62146779	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs113642575	chr1:62146784-62146785	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs553650623	chr1:62146788-62146789	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs59562457	chr1:62146789-62146790	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs578077460	chr1:62146833-62146834	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs371977020	chr1:62146834-62146835	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs76794916	chr1:62146961-62146962	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs181393594	chr1:62146962-62146963	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs537110429	chr1:62146966-62146967	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs11539585	chr1:62147019-62147020	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs545171070	chr1:62147045-62147046	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs538435816	chr1:62147085-62147086	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs543373329	chr1:62147095-62147096	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs572188821	chr1:62147100-62147101	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs560719998	chr1:62147109-62147110	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs10493311	chr1:62147149-62147150	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs572246455	chr1:62147254-62147255	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs542647082	chr1:62147260-62147261	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs575873882	chr1:62147297-62147298	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs1064488	chr1:62147343-62147344	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs542973982	chr1:62147347-62147348	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs542583382	chr1:62147368-62147369	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs554565039	chr1:62147403-62147404	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576219126	chr1:62147405-62147406	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs549563407	chr1:62147411-62147412	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs543513656	chr1:62147437-62147438	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs1064487	chr1:62147446-62147447	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs142777138	chr1:62147450-62147451	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs1064486	chr1:62147458-62147459	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs1064485	chr1:62147514-62147515	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:94)

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
Breast cancer	16620391	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
CNS Malformation Syndrome	17530927	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Colorectal cancer	20459617	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:271 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62103400-62146400	Weak transcription	Gastric	stomach
2	chr1:62120400-62148200	Weak transcription	Aorta	Aorta
3	chr1:62126000-62148800	Weak transcription	Left Ventricle	heart
4	chr1:62126000-62165200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:62131600-62151400	Weak transcription	Lung	lung
6	chr1:62131600-62163800	Weak transcription	Thymus	Thymus
7	chr1:62134800-62164400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:62134800-62164400	Weak transcription	Right Ventricle	heart
9	chr1:62135000-62165000	Weak transcription	Brain Germinal Matrix	brain
10	chr1:62135400-62146200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:62136000-62151200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:62136000-62153400	Weak transcription	NHDF-Ad	bronchial
13	chr1:62136600-62151800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:62136800-62173800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:62137000-62146200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:62137400-62146200	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:62138000-62146200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:62138400-62146200	Weak transcription	Esophagus	oesophagus
19	chr1:62138600-62148000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:62138800-62146200	Weak transcription	Fetal Lung	lung
21	chr1:62138800-62146200	Weak transcription	HMEC	breast
22	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
23	chr1:62139800-62146200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:62139800-62146200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:62140000-62189000	Weak transcription	NHLF	lung
26	chr1:62140200-62163800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:62141600-62146200	Weak transcription	GM12878-XiMat	blood
28	chr1:62142200-62149400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:62142400-62146200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:62142600-62147400	Weak transcription	Brain Anterior Caudate	brain
31	chr1:62142800-62148200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:62142800-62149400	Weak transcription	Small Intestine	intestine
33	chr1:62142800-62157800	Weak transcription	A549	lung
34	chr1:62142800-62172200	Weak transcription	Ovary	ovary
35	chr1:62142800-62188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:62143000-62147400	Weak transcription	Fetal Intestine Small	intestine
37	chr1:62143000-62148200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:62143000-62151200	Weak transcription	Fetal Stomach	stomach
39	chr1:62143200-62157800	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:62143200-62164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:62143400-62146200	Weak transcription	Primary B cells from cord blood	blood
42	chr1:62143400-62146200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:62143400-62153000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:62143600-62163400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:62143800-62148200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:62143800-62152600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:62143800-62165600	Weak transcription	Stomach Mucosa	stomach
48	chr1:62143800-62170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:62144000-62147400	Weak transcription	Fetal Kidney	kidney
50	chr1:62144000-62153000	Strong transcription	Primary monocytes fromperipheralblood	blood

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