Variant report

Variant	esv3394908
Chromosome Location	chr3:195890255-195893553
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195868011..195869690-chr3:195889023..195890635,2	MCF-7	breast:
2	chr3:195883008..195885288-chr3:195887358..195890307,2	K562	blood:
3	chr3:195807555..195809737-chr3:195889457..195892454,2	K562	blood:
4	chr3:195868179..195870899-chr3:195889538..195893919,5	K562	blood:
5	chr3:195869399..195874058-chr3:195891436..195894559,4	K562	blood:
6	chr3:195823642..195825667-chr3:195890214..195892220,2	K562	blood:
7	chr3:195806967..195809789-chr3:195888733..195890950,3	MCF-7	breast:
8	chr3:195890135..195892758-chr3:195896649..195899546,2	K562	blood:
9	chr3:195886180..195890208-chr3:195892653..195895699,4	K562	blood:
10	chr3:195804713..195809002-chr3:195892518..195897097,4	K562	blood:
11	chr3:195805984..195810331-chr3:195892473..195900125,13	K562	blood:
12	chr3:195890392..195892758-chr3:195896649..195898282,2	K562	blood:
13	chr3:195867258..195871811-chr3:195887693..195891038,5	K562	blood:
14	chr3:195807237..195809801-chr3:195891488..195894845,3	MCF-7	breast:
15	chr3:195806752..195810300-chr3:195885348..195891708,10	K562	blood:
16	chr3:195854415..195856195-chr3:195888995..195891354,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000072274	chromatin interactions
ENSG00000224652	chromatin interactions

Extended variants
information (count: 182 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:182 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs554238220	chr3:195890264-195890265	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs528952026	chr3:195890283-195890284	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs201255534	chr3:195890323-195890324	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs62410502	chr3:195890410-195890411	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs573399775	chr3:195890416-195890417	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs540739723	chr3:195890434-195890435	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs572403581	chr3:195890437-195890438	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs141634399	chr3:195890462-195890463	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs7372337	chr3:195890468-195890469	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs7612433	chr3:195890471-195890472	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs373899337	chr3:195890493-195890494	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs71323703	chr3:195890527-195890528	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs562305925	chr3:195890597-195890598	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs62410503	chr3:195890598-195890599	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs541697818	chr3:195890624-195890625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs559762191	chr3:195890635-195890636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs138420829	chr3:195890672-195890673	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs62410504	chr3:195890678-195890679	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs564230062	chr3:195890694-195890695	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs531275329	chr3:195890731-195890732	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs149605547	chr3:195890749-195890750	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs377730051	chr3:195890750-195890751	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs62410505	chr3:195890755-195890756	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs529662317	chr3:195890794-195890795	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs570529742	chr3:195890813-195890814	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs188700910	chr3:195890814-195890815	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs539826868	chr3:195890838-195890839	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs557836092	chr3:195890869-195890870	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs144402578	chr3:195890915-195890916	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs537130798	chr3:195890999-195891000	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs181079180	chr3:195891000-195891001	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs73891210	chr3:195891113-195891114	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs386670138	chr3:195891160-195891161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs116833875	chr3:195891161-195891162	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs572199481	chr3:195891181-195891182	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs186266031	chr3:195891210-195891211	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs563911352	chr3:195891232-195891233	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs372248335	chr3:195891247-195891248	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs189029046	chr3:195891250-195891251	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs77767561	chr3:195891275-195891276	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs148790598	chr3:195891295-195891296	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs529523229	chr3:195891311-195891312	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs372152914	chr3:195891320-195891321	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs546514014	chr3:195891334-195891335	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs113741648	chr3:195891341-195891342	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs547968081	chr3:195891363-195891364	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs141431673	chr3:195891403-195891404	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs533422141	chr3:195891408-195891409	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs568529976	chr3:195891415-195891416	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs201333253	chr3:195891421-195891422	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:188 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195874200-195892000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:195883400-195904400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:195887200-195890400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:195887200-195890600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:195887200-195890800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:195887200-195891600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:195887200-195893000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:195887400-195890600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:195887400-195890800	Weak transcription	Esophagus	oesophagus
10	chr3:195887400-195891200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:195887400-195891400	Weak transcription	Fetal Lung	lung
12	chr3:195887400-195891600	Weak transcription	Gastric	stomach
13	chr3:195887600-195890400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:195887600-195890400	Weak transcription	Adipose Nuclei	Adipose
15	chr3:195887600-195890400	Weak transcription	Liver	Liver
16	chr3:195887600-195890400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:195887600-195890400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:195887600-195890600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:195887600-195891400	Weak transcription	Fetal Kidney	kidney
20	chr3:195887600-195892800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:195887600-195905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:195887800-195890400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:195887800-195890400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:195887800-195890400	Weak transcription	Small Intestine	intestine
25	chr3:195887800-195890600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:195887800-195896800	Weak transcription	Primary B cells from cord blood	blood
27	chr3:195888000-195890400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:195888000-195890400	Weak transcription	K562	blood
29	chr3:195888000-195891200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:195888200-195890400	Weak transcription	HSMM	muscle
31	chr3:195888600-195893200	Enhancers	Stomach Mucosa	stomach
32	chr3:195889400-195890800	Enhancers	Placenta	Placenta
33	chr3:195889600-195890400	Enhancers	Hela-S3	cervix
34	chr3:195889600-195891000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:195889600-195891800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:195889600-195891800	Enhancers	Fetal Intestine Large	intestine
37	chr3:195889600-195892600	Enhancers	Pancreas	Pancrea
38	chr3:195890000-195895800	Weak transcription	Dnd41	blood
39	chr3:195890200-195890400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:195890200-195890400	Bivalent Enhancer	HepG2	liver
41	chr3:195890200-195890600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:195890200-195891000	Enhancers	Fetal Muscle Leg	muscle
43	chr3:195890200-195891000	Enhancers	Fetal Thymus	thymus
44	chr3:195890200-195891200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:195890200-195891400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:195890200-195891600	Enhancers	Colonic Mucosa	Colon
47	chr3:195890200-195892000	Enhancers	Fetal Intestine Small	intestine
48	chr3:195890400-195890600	Enhancers	HSMM	muscle
49	chr3:195890400-195890800	Enhancers	Liver	Liver
50	chr3:195890400-195891000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links