Variant report

Variant	esv3498434
Chromosome Location	chr3:109640366-109640865
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	EP300	chr3:109640393-109640719	SK-N-SH_RA	brain:	n/a	n/a
2	PBX3	chr3:109640323-109640868	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr3:109640337-109640877	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr3:109640496-109640885	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr3:109640471-109640769	H1-neurons	neurons:	n/a	n/a
6	REST	chr3:109640257-109640951	H1-neurons	neurons:	n/a	n/a
7	TCF12	chr3:109640340-109640932	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000214380	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs185343030	chr3:109640380-109640381	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs656177	chr3:109640447-109640448	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs200224039	chr3:109640453-109640454	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs527760307	chr3:109640488-109640489	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs547517076	chr3:109640489-109640490	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs561134942	chr3:109640492-109640493	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs533034061	chr3:109640502-109640503	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs530273571	chr3:109640509-109640510	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs190593026	chr3:109640510-109640511	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs182816762	chr3:109640543-109640544	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs656615	chr3:109640548-109640549	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs187896708	chr3:109640578-109640579	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs17720662	chr3:109640616-109640617	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs191940123	chr3:109640632-109640633	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs548563249	chr3:109640692-109640693	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs529070122	chr3:109640723-109640724	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs75616392	chr3:109640746-109640747	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs138672238	chr3:109640839-109640840	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs34848487	chr3:109640852-109640853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs570383831	chr3:109640859-109640860	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

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
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	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
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18765545	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Multiple myeloma	17550852	CNVD
Ductal carcinoma	22052326	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109630000-109642400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:109637400-109645200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:109637800-109640600	Weak transcription	A549	lung
4	chr3:109639800-109641000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:109640000-109640800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:109640400-109640600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:109640400-109640600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:109640400-109640800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:109640400-109640800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:109640400-109640800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:109640400-109640800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:109640600-109641000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:109640600-109641400	Enhancers	Fetal Lung	lung
14	chr3:109640600-109641600	Enhancers	Dnd41	blood
15	chr3:109640600-109641800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:109640600-109644400	Enhancers	A549	lung
17	chr3:109640800-109641200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:109640800-109642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:109640800-109646000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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