Variant report

Variant	nsv875616
Chromosome Location	chr2:190650460-190656614
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:190654554-190654665	HepG2	liver:	n/a	chr2:190654619-190654630 chr2:190654620-190654631 chr2:190654619-190654630
2	MXI1	chr2:190646968-190650605	SK-N-SH	brain:	n/a	n/a
3	MYC	chr2:190655651-190655851	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr2:190650362-190650776	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:190651169-190651254	K562	blood:	n/a	n/a
6	POLR2A	chr2:190648034-190650548	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr2:190650129-190650820	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr2:190652387-190652399	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr2:190651145-190651345	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr2:190648112-190650548	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:190652022-190652295	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr2:190654991-190655191	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr2:190648136-190651362	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:190651101-190651135	K562	blood:	n/a	n/a
15	POLR2A	chr2:190648053-190650549	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr2:190647769-190650571	GM12891	blood:	n/a	n/a
17	POLR2A	chr2:190654154-190654342	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr2:190650933-190650937	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr2:190648075-190650574	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:190654312-190654424	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:190655333-190655518	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr2:190650835-190650931	K562	blood:	n/a	n/a
23	POLR2A	chr2:190655062-190655114	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:190650732-190650845	H1-hESC	embryonic stem cell:	n/a	n/a
25	RUNX3	chr2:190656385-190656723	GM12878	blood:	n/a	n/a
26	STAT3	chr2:190654571-190654682	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr2:190650933-190651235	MCF10A-Er-Src	breast:	n/a	n/a
28	TCF7L2	chr2:190652473-190652771	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:190651111..190653686-chr2:190669212..190673503,3	K562	blood:
2	chr2:190624834..190630334-chr2:190647529..190650706,8	K562	blood:
3	chr2:190649682..190653858-chr2:190657943..190661151,4	K562	blood:
4	chr2:190524918..190527666-chr2:190648010..190650648,4	MCF-7	breast:
5	chr2:190631446..190641228-chr2:190647618..190650786,10	MCF-7	breast:
6	chr2:190624834..190631096-chr2:190647637..190651740,7	K562	blood:
7	chr2:190524324..190528374-chr2:190645867..190651485,5	K562	blood:
8	chr2:190632138..190639565-chr2:190646675..190650810,8	K562	blood:
9	chr2:190652358..190654600-chr2:190658326..190660113,2	K562	blood:
10	chr2:190615675..190618614-chr2:190648414..190651811,3	K562	blood:
11	chr2:190647276..190650554-chr2:190651285..190655596,9	MCF-7	breast:
12	chr2:190626395..190628968-chr2:190652066..190655379,3	K562	blood:
13	chr2:190626523..190630050-chr2:190647058..190650887,5	MCF-7	breast:
14	chr2:190523468..190528374-chr2:190647262..190651485,5	K562	blood:
15	chr2:190626375..190630628-chr2:190647839..190651386,6	MCF-7	breast:

No data

Variant related genes	Relation type
ORMDL1	TF binding region
PMS1	TF binding region
ENSG00000128694	chromatin interactions
ENSG00000138381	chromatin interactions
ENSG00000253559	chromatin interactions
ENSG00000223249	chromatin interactions
ENSG00000064933	chromatin interactions
ENSG00000273240	chromatin interactions
ENSG00000128699	chromatin interactions

Extended variants
information (count: 261 )
Associated
traits (count: 48 )

Variant overlapped rSNPs/rCNVs (count:261 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs5742941	chr2:190650460-190650461	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
2	rs373008957	chr2:190650461-190650462	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
3	rs376068137	chr2:190650462-190650463	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
4	rs553117359	chr2:190650507-190650508	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
5	rs568494828	chr2:190650517-190650518	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
6	rs535586763	chr2:190650557-190650558	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
7	rs5742942	chr2:190650579-190650580	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
8	rs575143348	chr2:190650584-190650585	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
9	rs375297893	chr2:190650613-190650614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
10	rs5742943	chr2:190650621-190650622	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs186231059	chr2:190650677-190650678	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
12	rs5742944	chr2:190650682-190650683	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs539812862	chr2:190650754-190650755	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
14	rs561527302	chr2:190650774-190650775	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
15	rs566596198	chr2:190650803-190650804	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
16	rs377301840	chr2:190650856-190650857	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
17	rs573637393	chr2:190650919-190650920	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
18	rs4666784	chr2:190650930-190650931	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs529390851	chr2:190650961-190650962	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs563902084	chr2:190651051-190651052	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs531165600	chr2:190651061-190651062	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
22	rs550473518	chr2:190651063-190651064	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
23	rs5742946	chr2:190651065-190651066	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
24	rs564744501	chr2:190651070-190651071	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
25	rs528800292	chr2:190651109-190651110	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
26	rs5742947	chr2:190651167-190651168	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
27	rs373762737	chr2:190651224-190651225	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
28	rs527461568	chr2:190651245-190651246	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
29	rs568402805	chr2:190651248-190651249	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
30	rs367596102	chr2:190651279-190651280	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
31	rs191326179	chr2:190651282-190651283	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
32	rs550824434	chr2:190651283-190651284	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
33	rs568694596	chr2:190651304-190651305	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
34	rs182695585	chr2:190651334-190651335	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
35	rs551677023	chr2:190651342-190651343	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
36	rs557553082	chr2:190651351-190651352	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
37	rs187865058	chr2:190651384-190651385	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
38	rs5742948	chr2:190651392-190651393	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
39	rs4666785	chr2:190651440-190651441	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs5742949	chr2:190651499-190651500	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs5742950	chr2:190651504-190651505	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
42	rs562536851	chr2:190651515-190651516	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
43	rs190912907	chr2:190651543-190651544	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
44	rs5742951	chr2:190651549-190651550	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
45	rs564679146	chr2:190651553-190651554	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
46	rs5742952	chr2:190651574-190651575	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs547026843	chr2:190651633-190651634	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
48	rs112415673	chr2:190651634-190651635	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
49	rs5742953	chr2:190651671-190651672	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
50	rs529303172	chr2:190651683-190651684	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:48)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
Colorectal cancer	16272173	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Glioblastoma	21080181	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Facial dysmorphism	20548289	CNVD
Mental retardation	20548289	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Breast cancer	21364760	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21183584	CNVD
Urothelial carcinoma	21177765	CNVD
Ovarian cancer	21720365	CNVD
Immune disease	21076436	CNVD
Immune disease	21042300	CNVD
Colorectal cancer	16912164	CNVD

Chromatin state (count:327 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190647400-190650600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr2:190647400-190651200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:190647600-190650600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:190647600-190650600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:190647600-190650600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:190647600-190650600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:190647600-190650600	Active TSS	Muscle Satellite Cultured Cells	--
8	chr2:190647600-190650600	Active TSS	NHLF	lung
9	chr2:190647600-190651000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:190647800-190650600	Active TSS	Fetal Brain Female	brain
11	chr2:190647800-190650800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:190648200-190650600	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr2:190649000-190651000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:190649200-190650600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:190649600-190650600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:190649600-190650800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:190649600-190656200	Weak transcription	Spleen	Spleen
18	chr2:190649600-190658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:190649800-190650600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr2:190649800-190650600	Flanking Active TSS	HUVEC	blood vessel
21	chr2:190649800-190650600	Flanking Active TSS	Osteobl	bone
22	chr2:190649800-190651000	Flanking Active TSS	Dnd41	blood
23	chr2:190649800-190657600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:190649800-190658600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:190649800-190662200	Weak transcription	Aorta	Aorta
26	chr2:190649800-190662200	Weak transcription	Left Ventricle	heart
27	chr2:190649800-190662800	Weak transcription	Lung	lung
28	chr2:190649800-190667200	Weak transcription	Pancreas	Pancrea
29	chr2:190649800-190675200	Weak transcription	Esophagus	oesophagus
30	chr2:190649800-190713400	Weak transcription	Gastric	stomach
31	chr2:190650000-190650600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:190650000-190650600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:190650000-190650600	Transcr. at gene 5' and 3'	A549	lung
34	chr2:190650000-190650600	Flanking Active TSS	HMEC	breast
35	chr2:190650000-190650800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr2:190650000-190650800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:190650000-190650800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:190650000-190650800	Flanking Active TSS	HepG2	liver
39	chr2:190650000-190651000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:190650000-190651000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:190650000-190656000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:190650000-190657000	Weak transcription	Placenta	Placenta
43	chr2:190650000-190688200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:190650200-190650600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:190650200-190650600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:190650200-190650600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:190650200-190650600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:190650200-190650600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:190650200-190650600	Enhancers	Fetal Lung	lung
50	chr2:190650200-190650600	Enhancers	Skeletal Muscle Male	skeletal muscle

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