Variant report

Variant	nsv215442
Chromosome Location	chr2:39676634-39681883
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:17)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr2:39676600-39676804	HepG2	liver:	n/a	n/a
2	CEBPB	chr2:39676550-39676656	HepG2	liver:	n/a	n/a
3	CEBPB	chr2:39676474-39676784	HepG2	liver:	n/a	n/a
4	EP300	chr2:39676700-39676720	HepG2	liver:	n/a	n/a
5	EP300	chr2:39676534-39676873	HepG2	liver:	n/a	n/a
6	EP300	chr2:39676537-39676789	HepG2	liver:	n/a	n/a
7	FOXA1	chr2:39676525-39676830	HepG2	liver:	n/a	n/a
8	GATA3	chr2:39679057-39679564	SK-N-SH	brain:	n/a	n/a
9	HDAC2	chr2:39676528-39676870	HepG2	liver:	n/a	n/a
10	HNF4A	chr2:39676553-39676953	HepG2	liver:	n/a	n/a
11	HNF4A	chr2:39676554-39676893	HepG2	liver:	n/a	n/a
12	MBD4	chr2:39676464-39676960	HepG2	liver:	n/a	n/a
13	MYBL2	chr2:39676318-39677001	HepG2	liver:	n/a	n/a
14	MYC	chr2:39678160-39678360	MCF10A-Er-Src	breast:	n/a	n/a
15	NFIC	chr2:39676456-39676940	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:39676869-39676958	MCF-7	breast:	n/a	n/a
17	POLR2A	chr2:39676653-39676914	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:39676935-39676962	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:39676526-39676679	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr2:39676672-39676842	HepG2	liver:	n/a	n/a
21	RCOR1	chr2:39676711-39676720	HepG2	liver:	n/a	n/a
22	REST	chr2:39676519-39676653	H1-hESC	embryonic stem cell:	n/a	n/a
23	RXRA	chr2:39676514-39676811	HepG2	liver:	n/a	n/a
24	SMC3	chr2:39676659-39676813	HepG2	liver:	n/a	n/a
25	SP1	chr2:39676363-39676962	HepG2	liver:	n/a	n/a
26	TEAD4	chr2:39676426-39676960	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39662826..39665276-chr2:39681866..39683470,2	MCF-7	breast:
2	chr2:39668408..39675131-chr2:39676739..39679699,8	K562	blood:
3	chr2:39678426..39680083-chr2:39696390..39697940,2	MCF-7	breast:
4	chr2:39673263..39677123-chr2:39692250..39696646,6	MCF-7	breast:
5	chr2:39676819..39680637-chr2:39680981..39683418,4	K562	blood:
6	chr2:39669445..39671277-chr2:39681735..39683817,2	K562	blood:

(count:17 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-1	chr2:39681438-39681867	ENSG00000231312.2
2	lnc-TMEM178-1	chr2:39680980-39681072	ENSG00000231312.2
3	lnc-TMEM178-1	chr2:39681460-39681506	NONHSAT070243
4	lnc-TMEM178-1	chr2:39681460-39681506	NONHSAT070242
5	lnc-TMEM178-1	chr2:39681063-39681072	ENSG00000231312.2
6	lnc-TMEM178-1	chr2:39681438-39681506	ENSG00000231312.2
7	lnc-TMEM178-1	chr2:39681440-39681506	NONHSAT070240
8	lnc-TMEM178-1	chr2:39680980-39681072	ENSG00000231312.2
9	lnc-TMEM178-1	chr2:39681438-39681506	NONHSAT070239
10	lnc-TMEM178-1	chr2:39681438-39681506	ENSG00000231312.2
11	lnc-TMEM178-1	chr2:39680980-39681072	ENSG00000231312.2
12	lnc-TMEM178-1	chr2:39681457-39681506	NONHSAT070241
13	lnc-TMEM178-1	chr2:39681438-39681506	ENSG00000231312.2
14	lnc-TMEM178-1	chr2:39680981-39681065	NONHSAT070232
15	lnc-TMEM178-1	chr2:39680980-39681072	ENSG00000231312.2
16	lnc-TMEM178-4	chr2:39680010-39680916	l_1814_chr2:39518006-39558253_76bGuttman_hLF
17	lnc-TMEM178-1	chr2:39681438-39681506	ENSG00000231312.2

No data

Variant related genes	Relation type
ENSG00000231312	TF binding region
ENSG00000011566	chromatin interactions
ENSG00000231312	chromatin interactions

Extended variants
information (count: 193 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:193 , 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	rs77849792	chr2:39676647-39676648	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs200663066	chr2:39676650-39676651	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs56833014	chr2:39676651-39676652	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs143143037	chr2:39676675-39676676	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs112224258	chr2:39676711-39676712	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs574759695	chr2:39676766-39676767	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs147404209	chr2:39676767-39676768	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs185907024	chr2:39676768-39676769	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs367552346	chr2:39676840-39676841	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs114520761	chr2:39676843-39676844	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs142457451	chr2:39676846-39676847	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs70957111	chr2:39676856-39676857	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs572589405	chr2:39676871-39676872	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs111608310	chr2:39676883-39676884	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs527775738	chr2:39676927-39676928	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs189632793	chr2:39676989-39676990	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs530196828	chr2:39677024-39677025	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs543099532	chr2:39677047-39677048	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs111832390	chr2:39677061-39677062	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs561560187	chr2:39677065-39677066	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs528881673	chr2:39677076-39677077	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs148044823	chr2:39677084-39677085	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs373671125	chr2:39677119-39677120	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs181211464	chr2:39677252-39677253	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs551574957	chr2:39677259-39677260	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs185772365	chr2:39677265-39677266	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs141766673	chr2:39677285-39677286	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs556672973	chr2:39677319-39677320	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs568406764	chr2:39677332-39677333	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs11690102	chr2:39677333-39677334	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs535829530	chr2:39677344-39677345	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs554177262	chr2:39677373-39677374	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs113820590	chr2:39677398-39677399	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs535671701	chr2:39677402-39677403	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs190531851	chr2:39677438-39677439	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs553603853	chr2:39677452-39677453	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs6544229	chr2:39677456-39677457	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs546004673	chr2:39677493-39677494	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs10199459	chr2:39677509-39677510	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs576211567	chr2:39677567-39677568	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs377559266	chr2:39677581-39677582	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs539756090	chr2:39677586-39677587	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs370129189	chr2:39677684-39677685	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs543162391	chr2:39677722-39677723	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs111261570	chr2:39677732-39677733	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs561812497	chr2:39677739-39677740	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs528890627	chr2:39677762-39677763	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs540976232	chr2:39677766-39677767	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs559411016	chr2:39677768-39677769	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs58704884	chr2:39677793-39677794	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16272173	CNVD

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665600-39681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:39665600-39684200	Weak transcription	Lung	lung
4	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
5	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
7	chr2:39666000-39681200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:39666200-39681400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:39666600-39682200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:39666800-39677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:39666800-39681000	Weak transcription	Brain Substantia Nigra	brain
13	chr2:39666800-39681600	Weak transcription	Ovary	ovary
14	chr2:39667000-39681400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:39667000-39681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
17	chr2:39667200-39685200	Weak transcription	NHEK	skin
18	chr2:39667200-39694600	Weak transcription	NHLF	lung
19	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
20	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
21	chr2:39667400-39682000	Weak transcription	HSMM	muscle
22	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:39668200-39681400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:39668200-39684800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:39668200-39685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:39668200-39694800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:39668200-39696800	Weak transcription	Right Ventricle	heart
29	chr2:39668400-39677000	Weak transcription	K562	blood
30	chr2:39670400-39682800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:39670400-39685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:39670800-39684800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:39671000-39682200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:39671200-39681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:39671200-39685000	Weak transcription	Aorta	Aorta
36	chr2:39671600-39682600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:39671800-39682000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:39672000-39681400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:39672200-39681400	Weak transcription	Adipose Nuclei	Adipose
40	chr2:39672200-39684600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:39672600-39681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:39673400-39681000	Weak transcription	Liver	Liver
43	chr2:39673600-39681000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:39674800-39678800	Enhancers	HepG2	liver
45	chr2:39675000-39696400	Weak transcription	Fetal Kidney	kidney
46	chr2:39675200-39677800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:39675200-39680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:39675200-39682600	Weak transcription	Osteobl	bone
49	chr2:39675200-39682800	Weak transcription	HMEC	breast
50	chr2:39675200-39686000	Weak transcription	NHDF-Ad	bronchial

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