Variant report

Variant	esv3323199
Chromosome Location	chr2:134024082-134025280
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154946346..154946996-chr2:134023337..134024323,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR39-4	chr2:134024845-134024996	ENSG00000226953
2	lnc-GPR39-4	chr2:134024845-134024996	ENSG00000226953.3
3	lnc-GPR39-4	chr2:134024845-134024996	NR_110294
4	lnc-GPR39-4	chr2:134024845-134024996	ENSG00000226953

Variant related genes	Relation type
ENSG00000160691	chromatin interactions
SMCR7L	miRNA target sites
NFKB1	miRNA target sites

Extended variants
information (count: 29 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs138136745	chr2:134024120-134024121	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs576006820	chr2:134024122-134024123	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs536909849	chr2:134024172-134024173	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs558896116	chr2:134024201-134024202	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs76481368	chr2:134024256-134024257	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs77255099	chr2:134024263-134024264	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs559622159	chr2:134024271-134024272	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs572427252	chr2:134024300-134024301	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs143622251	chr2:134024415-134024416	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
10	rs561091640	chr2:134024566-134024567	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
11	rs114303232	chr2:134024688-134024689	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
12	rs543084944	chr2:134024701-134024702	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
13	rs565233712	chr2:134024734-134024735	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
14	rs532705999	chr2:134024748-134024749	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
15	rs558483599	chr2:134024758-134024759	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
16	rs188996373	chr2:134024818-134024819	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs370322763	chr2:134024822-134024823	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs566287697	chr2:134024832-134024833	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs535936066	chr2:134024834-134024835	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs192427384	chr2:134024839-134024840	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs138296197	chr2:134024872-134024873	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
22	rs377667829	chr2:134024873-134024874	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
23	rs140406334	chr2:134024884-134024885	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
24	rs537042994	chr2:134025073-134025074	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs558628151	chr2:134025074-134025075	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs559640810	chr2:134025088-134025089	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs184800987	chr2:134025144-134025145	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs139560111	chr2:134025225-134025226	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs188140979	chr2:134025247-134025248	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Hepatocellular carcinoma	16750200	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
lymphocytic leukemia	21291569	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Colorectal cancer	16272173	CNVD
myoclonus epilepsy	18472482	CNVD
Benign familial neonatal-infantile seizures	18472482	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Developmental delay	21147756	CNVD
Mental retardation	17621639	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Breast cancer	21509527	CNVD
Mental retardation	17124404	CNVD
Colorectal cancer	20459617	CNVD
Neuroticism	17667963	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:192 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134022400-134024200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:134022600-134024400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:134022800-134024200	Active TSS	Brain Substantia Nigra	brain
4	chr2:134022800-134024400	Active TSS	Placenta	Placenta
5	chr2:134022800-134025000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr2:134022800-134025000	Enhancers	Fetal Heart	heart
7	chr2:134022800-134025000	Active TSS	Hela-S3	cervix
8	chr2:134022800-134025200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:134023000-134024200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:134023000-134024400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:134023000-134024400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
12	chr2:134023000-134024400	Active TSS	Rectal Smooth Muscle	rectum
13	chr2:134023000-134024400	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr2:134023000-134024800	Active TSS	Left Ventricle	heart
15	chr2:134023000-134024800	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr2:134023000-134025000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr2:134023000-134025000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr2:134023000-134025200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:134023000-134025200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr2:134023000-134025200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr2:134023000-134025200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr2:134023000-134025200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:134023200-134024200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:134023200-134024400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr2:134023200-134024800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr2:134023200-134024800	Active TSS	Psoas Muscle	Psoas
27	chr2:134023200-134024800	Active TSS	Right Atrium	heart
28	chr2:134023200-134025200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr2:134023400-134024200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr2:134023400-134024200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:134023400-134024400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:134023400-134024400	Flanking Active TSS	Liver	Liver
33	chr2:134023400-134024400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr2:134023400-134024400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr2:134023400-134024600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:134023400-134025200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr2:134023600-134024200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:134023600-134024200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:134023600-134024200	Bivalent/Poised TSS	Fetal Lung	lung
40	chr2:134023600-134024400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:134023600-134024400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:134023600-134024800	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr2:134023600-134024800	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr2:134023600-134024800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:134023600-134024800	Active TSS	Brain Anterior Caudate	brain
46	chr2:134023600-134025000	Active TSS	Brain Angular Gyrus	brain
47	chr2:134023600-134025000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr2:134023600-134025000	Active TSS	A549	lung
49	chr2:134023600-134025000	Active TSS	NHLF	lung
50	chr2:134023600-134025200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links