Variant report

Variant	nsv511729
Chromosome Location	chr1:212470912-212472960
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:212472829-212472991	SH-SY5Y	brain:	n/a	n/a
2	NR2F2	chr1:212471184-212471571	K562	blood:	n/a	n/a
3	NR3C1	chr1:212471256-212471568	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212467247..212471909-chr1:212472711..212476183,6	K562	blood:
2	chr1:212464978..212469431-chr1:212471345..212474474,8	K562	blood:
3	chr1:212467247..212471909-chr1:212472711..212476183,6	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NENF-2	chr1:212470790-212471143	ENSG00000230063.1
2	lnc-TMEM206-3	chr1:212472837-212472967	ENSG00000234915.1
3	lnc-NENF-2	chr1:212472626-212472921	ENSG00000230063.1

No data

Variant related genes	Relation type
PPP2R5A	TF binding region
ENSG00000230063	chromatin interactions
ENSG00000066027	chromatin interactions

Extended variants
information (count: 44 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:44 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs537249766	chr1:212470932-212470933	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs188266107	chr1:212470951-212470952	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs567480338	chr1:212471031-212471032	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs568499051	chr1:212471059-212471060	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs56061076	chr1:212471158-212471159	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs78920543	chr1:212471165-212471166	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs56344268	chr1:212471167-212471168	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs183217528	chr1:212471174-212471175	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs535920695	chr1:212471204-212471205	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs373837325	chr1:212471234-212471235	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs368071137	chr1:212471294-212471295	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs28579866	chr1:212471394-212471395	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs544172791	chr1:212471479-212471480	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs200168250	chr1:212471484-212471485	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs554334137	chr1:212471487-212471488	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs28582469	chr1:212471720-212471721	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs563809628	chr1:212471812-212471813	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs577539217	chr1:212471817-212471818	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs564427288	chr1:212472263-212472264	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs578015615	chr1:212472290-212472291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs540362468	chr1:212472371-212472372	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs559526596	chr1:212472389-212472390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs183767788	chr1:212472466-212472467	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
24	rs28662023	chr1:212472512-212472513	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs550084370	chr1:212472521-212472522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs572387739	chr1:212472524-212472525	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs539486779	chr1:212472538-212472539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs558421811	chr1:212472569-212472570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs192103283	chr1:212472614-212472615	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs202173200	chr1:212472616-212472617	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs367780780	chr1:212472628-212472629	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs576613198	chr1:212472651-212472652	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs547956014	chr1:212472676-212472677	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs377306167	chr1:212472680-212472681	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs543714902	chr1:212472728-212472729	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs531051861	chr1:212472731-212472732	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs12137798	chr1:212472734-212472735	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs141382021	chr1:212472743-212472744	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs183545276	chr1:212472781-212472782	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs559058302	chr1:212472798-212472799	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs351389	chr1:212472872-212472873	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs144999970	chr1:212472891-212472892	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
43	rs563302192	chr1:212472946-212472947	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs530678976	chr1:212472947-212472948	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Multiple myeloma	16461302	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	17060936	CNVD
Atypical hemolytic uremic syndrome	19861685	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Medulloblastoma	16783165	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Holoprosencephaly	19184110	CNVD
Breast cancer	21069454	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212461000-212476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:212462000-212471200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:212462200-212471000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:212462200-212471000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:212462600-212471000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:212463800-212471000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:212463800-212471000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:212464200-212471200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:212464200-212483000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:212464600-212473000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:212464800-212480200	Weak transcription	Lung	lung
13	chr1:212464800-212483800	Weak transcription	Pancreas	Pancrea
14	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
15	chr1:212465000-212474800	Weak transcription	Osteobl	bone
16	chr1:212465000-212480200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:212465400-212475000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:212465400-212482800	Weak transcription	Fetal Lung	lung
19	chr1:212465800-212483200	Weak transcription	Dnd41	blood
20	chr1:212466200-212473000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:212466600-212479400	Weak transcription	NHEK	skin
23	chr1:212466600-212482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:212467000-212472800	Weak transcription	Primary B cells from cord blood	blood
26	chr1:212467000-212473400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:212467000-212480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:212467200-212474800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:212467200-212475000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:212467200-212481800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:212467400-212474800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:212467400-212480200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:212467400-212482800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:212467400-212526000	Weak transcription	A549	lung
35	chr1:212467600-212482800	Weak transcription	HepG2	liver
36	chr1:212468200-212471200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:212468800-212474200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:212468800-212476000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:212468800-212478200	Weak transcription	Fetal Intestine Small	intestine
40	chr1:212469000-212472600	Weak transcription	Fetal Heart	heart
41	chr1:212469000-212473200	Weak transcription	Small Intestine	intestine
42	chr1:212469000-212474800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:212469000-212480200	Weak transcription	Fetal Intestine Large	intestine
44	chr1:212469000-212483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:212469000-212483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:212469200-212474200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:212469400-212474400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:212469600-212473000	Weak transcription	Left Ventricle	heart
49	chr1:212469600-212473000	Weak transcription	Psoas Muscle	Psoas
50	chr1:212469600-212473400	Weak transcription	Right Ventricle	heart

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