Variant report

Variant	nsv589284
Chromosome Location	chr3:250758-269035
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr3:254017-254518	GM12878	blood:	n/a	n/a
2	ATF2	chr3:254098-254530	GM12878	blood:	n/a	n/a
3	BATF	chr3:254085-254416	GM12878	blood:	n/a	n/a
4	BATF	chr3:259675-259847	GM12878	blood:	n/a	n/a
5	BHLHE40	chr3:260263-260618	GM12878	blood:	n/a	n/a
6	BHLHE40	chr3:260829-261058	GM12878	blood:	n/a	n/a
7	CREB1	chr3:254049-254528	GM12878	blood:	n/a	n/a
8	CTCF	chr3:266691-266735	GM20000	blood:	n/a	n/a
9	EBF1	chr3:260927-261165	GM12878	blood:	n/a	chr3:261010-261021
10	EBF1	chr3:254125-254530	GM12878	blood:	n/a	n/a
11	EGR1	chr3:260837-260993	GM12878	blood:	n/a	chr3:260903-260917
12	EP300	chr3:260882-260922	GM12878	blood:	n/a	n/a
13	IKZF1	chr3:254051-254650	GM12878	blood:	n/a	n/a
14	JUN	chr3:253163-253648	K562	blood:	n/a	n/a
15	MAFF	chr3:255708-255996	HepG2	liver:	n/a	n/a
16	MAFK	chr3:255703-256035	HepG2	liver:	n/a	n/a
17	MAFK	chr3:255701-256022	HepG2	liver:	n/a	n/a
18	MAFK	chr3:255728-256000	IMR90	lung:	n/a	n/a
19	NFIC	chr3:254014-254551	GM12878	blood:	n/a	n/a
20	NFIC	chr3:259567-259959	GM12878	blood:	n/a	n/a
21	NFYB	chr3:259689-259948	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:268237-268389	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:259540-259953	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr3:254007-254638	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr3:268418-268428	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:255635-255734	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:253983-254585	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr3:254209-254554	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:254330-254460	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:254310-254436	GM12878	blood:	n/a	n/a
31	POU2F2	chr3:260395-260628	GM12878	blood:	n/a	n/a
32	RELA	chr3:254078-254554	GM18951	blood:	n/a	n/a
33	RELA	chr3:253987-254581	GM12891	blood:	n/a	n/a
34	RELA	chr3:254051-254523	GM12878	blood:	n/a	n/a
35	RELA	chr3:254117-254503	GM19193	blood:	n/a	n/a
36	RELA	chr3:254059-254536	GM19099	blood:	n/a	n/a
37	REST	chr3:253883-254679	H1-neurons	neurons:	n/a	n/a
38	REST	chr3:253757-254896	H1-neurons	neurons:	n/a	n/a
39	RFX5	chr3:255770-255904	HepG2	liver:	n/a	n/a
40	RUNX3	chr3:260752-261097	GM12878	blood:	n/a	n/a
41	RUNX3	chr3:254012-254473	GM12878	blood:	n/a	n/a
42	RUNX3	chr3:260361-260656	GM12878	blood:	n/a	n/a
43	RUNX3	chr3:259540-259939	GM12878	blood:	n/a	n/a
44	RUNX3	chr3:260267-260661	GM12878	blood:	n/a	n/a
45	RUNX3	chr3:259571-259846	GM12878	blood:	n/a	n/a
46	SETDB1	chr3:265101-265589	U2OS	brain:	n/a	n/a
47	SPI1	chr3:260791-260956	GM12878	blood:	n/a	n/a
48	SPI1	chr3:260767-260996	GM12891	blood:	n/a	n/a
49	SPI1	chr3:260781-260997	GM12891	blood:	n/a	n/a
50	SPI1	chr3:260838-260989	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTN6-7	chr3:254887-255362	NONHSAT087562

Variant related genes	Relation type
CHL1	TF binding region

Extended variants
information (count: 853 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:853 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9809528	chr3:250758-250759	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs34374128	chr3:250786-250787	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs568277474	chr3:250893-250894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs190270369	chr3:250903-250904	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs6790586	chr3:250912-250913	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs142291502	chr3:250923-250924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs566932392	chr3:250932-250933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs537188319	chr3:250983-250984	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs17006137	chr3:251004-251005	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs181877173	chr3:251005-251006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs369473561	chr3:251030-251031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs35394807	chr3:251069-251070	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs17006157	chr3:251075-251076	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs575233852	chr3:251082-251083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs73016741	chr3:251097-251098	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs563908924	chr3:251129-251130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs531121049	chr3:251132-251133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs552350330	chr3:251157-251158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs199789524	chr3:251229-251230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs202079436	chr3:251232-251233	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs80350980	chr3:251240-251241	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs528151788	chr3:251241-251242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs200294702	chr3:251247-251248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs546299124	chr3:251255-251256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs568025783	chr3:251257-251258	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs535049767	chr3:251264-251265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs550171958	chr3:251334-251335	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs568565744	chr3:251343-251344	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs186427559	chr3:251357-251358	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs79932543	chr3:251381-251382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs35847390	chr3:251393-251394	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs191145361	chr3:251396-251397	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs548579912	chr3:251410-251411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs112552156	chr3:251412-251413	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs371378609	chr3:251420-251421	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs13082190	chr3:251422-251423	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs112359985	chr3:251448-251449	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs563674108	chr3:251456-251457	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs78013178	chr3:251472-251473	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs367610811	chr3:251530-251531	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs142933154	chr3:251531-251532	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs139811744	chr3:251546-251547	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs571378097	chr3:251552-251553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs373487962	chr3:251614-251615	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs75052201	chr3:251625-251626	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs546789589	chr3:251627-251628	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs61046032	chr3:251647-251648	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs561609418	chr3:251669-251670	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs538723451	chr3:251674-251675	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs529153952	chr3:251680-251681	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:243600-252000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:244400-254200	Weak transcription	Brain Anterior Caudate	brain
3	chr3:244800-254200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:245400-252000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:246200-258600	Weak transcription	Fetal Brain Female	brain
6	chr3:249000-251600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:249000-251800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:250200-252400	Weak transcription	Fetal Brain Male	brain
9	chr3:251600-255400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:251800-255200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:252000-252200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:252000-252800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:252000-253000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:252200-252400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:252400-253000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:252400-253200	Enhancers	Fetal Brain Male	brain
17	chr3:252800-256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:253000-253400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:253000-254000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:253200-258200	Weak transcription	Fetal Brain Male	brain
21	chr3:253600-254600	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:253800-254000	Enhancers	GM12878-XiMat	blood
23	chr3:253800-254600	Enhancers	Primary B cells from cord blood	blood
24	chr3:254000-254400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:254000-254400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:254000-254400	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:254000-254600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:254000-255200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:254200-254400	Enhancers	Brain Germinal Matrix	brain
30	chr3:254200-254600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:254400-254600	Enhancers	Brain Anterior Caudate	brain
32	chr3:254400-255400	Weak transcription	GM12878-XiMat	blood
33	chr3:254400-258400	Weak transcription	Brain Germinal Matrix	brain
34	chr3:254600-258400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:255200-258400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:255400-265400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:257000-257200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr3:257200-258200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:258200-258600	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr3:258200-259400	Enhancers	Fetal Brain Male	brain
41	chr3:258400-258600	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:258400-258800	Enhancers	Brain Hippocampus Middle	brain
43	chr3:258400-259400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:258400-261400	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:258600-258800	Enhancers	Brain Germinal Matrix	brain
46	chr3:258600-259400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:258600-259400	Enhancers	Fetal Brain Female	brain
48	chr3:258600-259400	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr3:259200-259400	Enhancers	Esophagus	oesophagus
50	chr3:259200-260000	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links