Variant report

Variant	nsv525190
Chromosome Location	chr3:143899074-143909347
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	CEBPB	chr3:143906442-143906770	A549	lung:	n/a	chr3:143906601-143906612 chr3:143906603-143906612
2	CEBPB	chr3:143906399-143906788	IMR90	lung:	n/a	chr3:143906601-143906612 chr3:143906603-143906612
3	CEBPB	chr3:143906448-143906725	K562	blood:	n/a	chr3:143906601-143906612 chr3:143906603-143906612
4	CEBPB	chr3:143906424-143906761	HepG2	liver:	n/a	chr3:143906601-143906612 chr3:143906603-143906612
5	CTCF	chr3:143908636-143908709	GM12878	blood:	n/a	chr3:143908658-143908679 chr3:143908656-143908674
6	CTCF	chr3:143907240-143907390	GM12865	blood:	n/a	n/a
7	EP300	chr3:143906096-143906295	K562	blood:	n/a	n/a
8	FOS	chr3:143904196-143904502	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:143904339-143904366	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr3:143904007-143904434	MCF10A-Er-Src	breast:	n/a	n/a
11	FOXP2	chr3:143906598-143907067	SK-N-MC	brain:	n/a	n/a
12	MAFF	chr3:143906965-143906971	K562	blood:	n/a	n/a
13	MAFF	chr3:143906923-143907140	HepG2	liver:	n/a	chr3:143907006-143907024
14	MAFK	chr3:143899856-143900029	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAFK	chr3:143904000-143904248	HepG2	liver:	n/a	n/a
16	MAFK	chr3:143906874-143907164	IMR90	lung:	n/a	chr3:143907011-143907022 chr3:143907012-143907023 chr3:143907012-143907023
17	MAFK	chr3:143906842-143907176	HepG2	liver:	n/a	chr3:143907011-143907022 chr3:143907012-143907023 chr3:143907012-143907023
18	NR2F2	chr3:143906064-143906244	K562	blood:	n/a	n/a
19	NR2F2	chr3:143905945-143906440	K562	blood:	n/a	n/a
20	POLR2A	chr3:143906542-143907591	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr3:143909240-143909330	K562	blood:	n/a	n/a
22	RUNX3	chr3:143906663-143906932	GM12878	blood:	n/a	n/a
23	RUNX3	chr3:143906610-143906915	GM12878	blood:	n/a	n/a
24	SETDB1	chr3:143904113-143904546	U2OS	brain:	n/a	n/a
25	TAL1	chr3:143906055-143906310	K562	blood:	n/a	n/a
26	USF1	chr3:143906068-143906241	K562	blood:	n/a	n/a
27	ZNF143	chr3:143906768-143906823	GM12878	blood:	n/a	chr3:143906776-143906795 chr3:143906777-143906792
28	ZNF143	chr3:143908019-143908260	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:143890771..143894320-chr3:143898037..143901332,4	MCF-7	breast:
2	chr3:143902901..143904761-chr3:143930558..143932653,2	MCF-7	breast:
3	chr3:143900814..143902970-chr3:143905127..143907243,2	K562	blood:
4	chr3:143892804..143894519-chr3:143897127..143900073,2	K562	blood:

Variant related genes	Relation type
RNA5SP144	TF binding region
ENSG00000222778	chromatin interactions

Extended variants
information (count: 338 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:338 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13067831	chr3:143899074-143899075	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs189224266	chr3:143899089-143899090	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs182407475	chr3:143899111-143899112	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs7630725	chr3:143899145-143899146	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs550374933	chr3:143899151-143899152	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs562401937	chr3:143899228-143899229	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs571345883	chr3:143899303-143899304	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs369687870	chr3:143899317-143899318	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs529601578	chr3:143899319-143899320	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs547459983	chr3:143899364-143899365	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs200249409	chr3:143899385-143899386	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs372014322	chr3:143899445-143899446	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs551200537	chr3:143899457-143899458	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs565123790	chr3:143899529-143899530	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs372443755	chr3:143899589-143899590	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs56171473	chr3:143899608-143899609	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs536885496	chr3:143899620-143899621	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs555136898	chr3:143899650-143899651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs573647233	chr3:143899651-143899652	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs186581987	chr3:143899765-143899766	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs190214179	chr3:143899771-143899772	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs572366336	chr3:143899787-143899788	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs55835333	chr3:143899840-143899841	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs564449734	chr3:143899843-143899844	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs181917098	chr3:143899918-143899919	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs538885581	chr3:143900000-143900001	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs562260651	chr3:143900012-143900013	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs1550781	chr3:143900023-143900024	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs548117052	chr3:143900036-143900037	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs559959529	chr3:143900047-143900048	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs532819672	chr3:143900192-143900193	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs185625903	chr3:143900199-143900200	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs9822743	chr3:143900231-143900232	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs537150129	chr3:143900253-143900254	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs376060524	chr3:143900260-143900261	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs9822894	chr3:143900277-143900278	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs567132932	chr3:143900299-143900300	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs536512662	chr3:143900300-143900301	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs534476518	chr3:143900369-143900370	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs151072914	chr3:143900429-143900430	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs372729259	chr3:143900448-143900449	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs375948654	chr3:143900488-143900489	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs577846720	chr3:143900522-143900523	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs539482466	chr3:143900524-143900525	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs558122888	chr3:143900603-143900604	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs576507053	chr3:143900638-143900639	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs543934536	chr3:143900650-143900651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs554539435	chr3:143900731-143900732	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs140973299	chr3:143900738-143900739	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs574849203	chr3:143900745-143900746	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

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
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	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
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Adrenocortical carcinoma	18281524	CNVD
Breast cancer	21509527	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143896400-143902000	Enhancers	Fetal Intestine Large	intestine
2	chr3:143896800-143899800	Weak transcription	Liver	Liver
3	chr3:143897000-143902800	Enhancers	Fetal Intestine Small	intestine
4	chr3:143898400-143919000	Weak transcription	Ovary	ovary
5	chr3:143898600-143901400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:143898800-143899800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:143899200-143899400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:143899800-143900400	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:143899800-143900600	Enhancers	Liver	Liver
10	chr3:143900000-143900200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:143901400-143901600	Enhancers	Brain Hippocampus Middle	brain
12	chr3:143901600-143902000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:143904000-143904800	Enhancers	HSMM	muscle
14	chr3:143904400-143904800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:143904800-143906800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:143904800-143906800	Weak transcription	HSMM	muscle
17	chr3:143905800-143906800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:143906400-143908600	Enhancers	Dnd41	blood
19	chr3:143906600-143907000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:143906600-143907400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:143906600-143907600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:143906600-143908400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:143906600-143908600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:143906800-143907200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:143906800-143907400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:143906800-143907400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:143906800-143907400	Enhancers	HSMM	muscle
28	chr3:143906800-143907600	Enhancers	Primary T cells from cord blood	blood
29	chr3:143906800-143908000	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:143907000-143908200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:143907200-143907400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:143907200-143907400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:143907200-143907400	Enhancers	HSMMtube	muscle
34	chr3:143907200-143908000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:143907200-143908200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:143907200-143908400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:143907200-143908400	Enhancers	Brain Substantia Nigra	brain
38	chr3:143907400-143908000	Weak transcription	HSMM	muscle
39	chr3:143907400-143908400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:143907600-143908200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:143907800-143908200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr3:143907800-143908200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr3:143907800-143908200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:143907800-143908800	Enhancers	Brain Hippocampus Middle	brain
45	chr3:143908000-143908200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:143908000-143908200	Enhancers	HSMM	muscle
47	chr3:143908000-143908200	Enhancers	HSMMtube	muscle
48	chr3:143908000-143908200	Enhancers	NH-A	brain
49	chr3:143908000-143908600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:143908000-143908600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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