Variant report

Variant	esv33044
Chromosome Location	chr3:179688785-179691941
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	E2F4	chr3:179691231-179691578	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:179690845-179691251	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:179689147-179689355	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:179690933-179691302	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:179689138-179689714	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr3:179691029-179691072	MCF10A-Er-Src	breast:	n/a	n/a
7	MAFF	chr3:179689187-179689458	HepG2	liver:	n/a	chr3:179689323-179689341
8	MAFK	chr3:179689187-179689406	HepG2	liver:	n/a	chr3:179689324-179689339 chr3:179689324-179689340
9	MAFK	chr3:179689183-179689478	HepG2	liver:	n/a	chr3:179689324-179689339 chr3:179689324-179689340
10	POLR2A	chr3:179691076-179691311	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:179689495-179689570	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:179691899-179692196	Gliobla	brain:	n/a	n/a
13	STAT3	chr3:179691019-179691022	MCF10A-Er-Src	breast:	n/a	n/a
14	ZNF263	chr3:179691749-179692330	HEK293-T-REx	kidney:	n/a	chr3:179692101-179692110

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPL47-6	chr3:179689382-179689448	NONHSAT093424

Variant related genes	Relation type
PEX5L	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:98 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544417255	chr3:179688826-179688827	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
2	rs554602848	chr3:179688831-179688832	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
3	rs370874090	chr3:179688905-179688906	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
4	rs574838996	chr3:179688940-179688941	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
5	rs140923625	chr3:179688973-179688974	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
6	rs3030810	chr3:179688980-179688981	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
7	rs374504805	chr3:179688981-179688982	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
8	rs3836473	chr3:179688991-179688992	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
9	rs561370185	chr3:179688992-179688993	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
10	rs540763538	chr3:179689012-179689013	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
11	rs77201940	chr3:179689030-179689031	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
12	rs190096899	chr3:179689121-179689122	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
13	rs3774255	chr3:179689173-179689174	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs545751635	chr3:179689177-179689178	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
15	rs562788918	chr3:179689223-179689224	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
16	rs531496657	chr3:179689245-179689246	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
17	rs386668792	chr3:179689264-179689265	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
18	rs114098152	chr3:179689265-179689266	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
19	rs112376579	chr3:179689274-179689275	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
20	rs3774257	chr3:179689365-179689366	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs547501886	chr3:179689366-179689367	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
22	rs570328448	chr3:179689375-179689376	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
23	rs374485695	chr3:179689405-179689406	Weak transcription Enhancers Active TSS Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
24	rs180857912	chr3:179689406-179689407	Weak transcription Enhancers Active TSS Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
25	rs34102436	chr3:179689415-179689416	Weak transcription Enhancers Active TSS Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
26	rs569217258	chr3:179689506-179689507	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs538000917	chr3:179689556-179689557	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs111228011	chr3:179689597-179689598	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs560409284	chr3:179689631-179689632	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs184926447	chr3:179689680-179689681	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs6777029	chr3:179689701-179689702	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs554262469	chr3:179689751-179689752	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs577130840	chr3:179689809-179689810	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs9871887	chr3:179689821-179689822	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs562728420	chr3:179689822-179689823	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs576403253	chr3:179689863-179689864	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs36068769	chr3:179689878-179689879	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs151185619	chr3:179689917-179689918	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs561715591	chr3:179689966-179689967	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs527507076	chr3:179689971-179689972	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs547145733	chr3:179689976-179689977	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs9875854	chr3:179690000-179690001	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs140203249	chr3:179690035-179690036	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs150433099	chr3:179690073-179690074	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs549367552	chr3:179690098-179690099	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs371791055	chr3:179690130-179690131	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs79033980	chr3:179690132-179690133	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs538134211	chr3:179690141-179690142	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs548501501	chr3:179690199-179690200	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs138175466	chr3:179690210-179690211	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:72)

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	22032731	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
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Anaplastic thyroid cancer	17989125	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Ovarian cancer	18208621	CNVD
Thyroid cancer	17317825	CNVD
Thyroid cancer	17989125	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Breast cancer	21806811	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	19653912	CNVD
Myelofibrosis	22110671	CNVD
Prostate cancer	17217626	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Prostate cancer	18632612	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179686000-179691400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:179686400-179689400	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr3:179686400-179691800	Weak transcription	Osteobl	bone
4	chr3:179686600-179688800	Enhancers	Fetal Brain Male	brain
5	chr3:179686800-179692000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr3:179686800-179692200	Active TSS	Brain Substantia Nigra	brain
7	chr3:179687000-179689400	Active TSS	Brain Cingulate Gyrus	brain
8	chr3:179687400-179692200	Active TSS	Brain Anterior Caudate	brain
9	chr3:179687800-179691000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:179688000-179688800	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr3:179688000-179688800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:179688000-179688800	Enhancers	Fetal Thymus	thymus
13	chr3:179688000-179688800	Enhancers	Thymus	Thymus
14	chr3:179688200-179689000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:179688400-179690600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:179688400-179690800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:179688400-179692200	Active TSS	Brain Hippocampus Middle	brain
18	chr3:179688600-179690800	Weak transcription	GM12878-XiMat	blood
19	chr3:179688800-179689200	Weak transcription	Fetal Brain Male	brain
20	chr3:179688800-179690400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:179688800-179691400	Weak transcription	Fetal Thymus	thymus
22	chr3:179688800-179691600	Weak transcription	Thymus	Thymus
23	chr3:179688800-179692000	Active TSS	Brain Angular Gyrus	brain
24	chr3:179689000-179689400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:179689200-179689400	Enhancers	Fetal Brain Male	brain
26	chr3:179689400-179689600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:179689400-179690200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:179689400-179691200	Flanking Active TSS	Dnd41	blood
29	chr3:179689400-179710200	Weak transcription	Fetal Brain Male	brain
30	chr3:179689600-179690000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:179690200-179691800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:179690200-179692200	Active TSS	Brain Cingulate Gyrus	brain
33	chr3:179690400-179692200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:179690600-179691600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:179690800-179691000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:179690800-179691000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:179690800-179691800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:179690800-179691800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
39	chr3:179690800-179692200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:179690800-179692400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:179690800-179692600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:179691000-179691200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:179691000-179692000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:179691200-179691600	Weak transcription	GM12878-XiMat	blood
45	chr3:179691200-179692000	Active TSS	Dnd41	blood
46	chr3:179691400-179691600	Enhancers	Fetal Thymus	thymus
47	chr3:179691400-179692400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:179691400-179692400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr3:179691400-179692600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr3:179691600-179691800	Enhancers	Thymus	Thymus

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