Variant report

Variant	esv3402943
Chromosome Location	chr3:141686262-141689235
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	FOXA1	chr3:141686404-141686711	HepG2	liver:	n/a	n/a
2	FOXA2	chr3:141688562-141688727	HepG2	liver:	n/a	chr3:141688608-141688620 chr3:141688604-141688616
3	MYC	chr3:141688718-141688768	MCF-7	breast:	n/a	chr3:141688757-141688766 chr3:141688755-141688768 chr3:141688756-141688766 chr3:141688758-141688765 chr3:141688756-141688767
4	NRF1	chr3:141686751-141686772	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:141686744-141686760	K562	blood:	n/a	n/a
6	POLR2A	chr3:141688691-141688787	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:141688788-141688791	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:141688781-141688813	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:141688312-141688443	ProgFib	skin:	n/a	n/a
10	POLR2A	chr3:141688681-141688856	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141679111..141682072-chr3:141685599..141688176,2	K562	blood:

Variant related genes	Relation type
TFDP2	TF binding region

Extended variants
information (count: 165 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:165 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558564061	chr3:141686264-141686265	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs529933490	chr3:141686268-141686269	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs548494919	chr3:141686281-141686282	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs374464450	chr3:141686283-141686284	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs536069806	chr3:141686355-141686356	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs551762164	chr3:141686362-141686363	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs148824773	chr3:141686437-141686438	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs537136928	chr3:141686482-141686483	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs537571827	chr3:141686494-141686495	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs76758219	chr3:141686545-141686546	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs575011229	chr3:141686587-141686588	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs78931705	chr3:141686598-141686599	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs554491241	chr3:141686610-141686611	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs76486410	chr3:141686614-141686615	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs559792135	chr3:141686619-141686620	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs79421438	chr3:141686624-141686625	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs143483468	chr3:141686625-141686626	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs558205179	chr3:141686628-141686629	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs576574096	chr3:141686692-141686693	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs77575982	chr3:141686706-141686707	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs562524376	chr3:141686743-141686744	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs529948754	chr3:141686769-141686770	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs373261731	chr3:141686837-141686838	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs541746508	chr3:141686852-141686853	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs560352779	chr3:141686893-141686894	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs76881227	chr3:141686902-141686903	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs564921817	chr3:141686942-141686943	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs570129590	chr3:141686985-141686986	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs113027298	chr3:141686998-141686999	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs549875281	chr3:141686999-141687000	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs35807930	chr3:141687034-141687035	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs568556909	chr3:141687042-141687043	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs540987936	chr3:141687082-141687083	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs560996493	chr3:141687111-141687112	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs570914695	chr3:141687131-141687132	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs568970500	chr3:141687145-141687146	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs63125262	chr3:141687156-141687157	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs574342000	chr3:141687170-141687171	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs578060458	chr3:141687171-141687172	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs12330323	chr3:141687223-141687224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs185577101	chr3:141687236-141687237	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs62637153	chr3:141687245-141687246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs62637154	chr3:141687247-141687248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs60401561	chr3:141687253-141687254	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs62637155	chr3:141687255-141687256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs62637156	chr3:141687264-141687265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs190534320	chr3:141687265-141687266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs182020125	chr3:141687266-141687267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs575713662	chr3:141687276-141687277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs528324350	chr3:141687287-141687288	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:52)

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
Lung cancer	16740712	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
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:199 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141659200-141696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:141660600-141698200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:141666000-141697600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:141666400-141687200	Strong transcription	Dnd41	blood
6	chr3:141668000-141686600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:141668600-141688600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:141669600-141696800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:141671600-141697400	Weak transcription	Gastric	stomach
10	chr3:141671800-141686400	Weak transcription	HepG2	liver
11	chr3:141671800-141691200	Weak transcription	Spleen	Spleen
12	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
13	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
14	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
15	chr3:141672000-141697000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:141672000-141700000	Weak transcription	Small Intestine	intestine
17	chr3:141672400-141688600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:141674400-141688000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:141674400-141690200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:141674400-141708000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:141674600-141700400	Weak transcription	Esophagus	oesophagus
22	chr3:141674600-141712600	Weak transcription	Fetal Brain Male	brain
23	chr3:141675400-141687000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:141675400-141687200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:141675600-141687200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:141675600-141687200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:141675600-141687200	Strong transcription	Thymus	Thymus
28	chr3:141675800-141687200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:141676000-141687000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:141676000-141687000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:141676000-141687000	Strong transcription	Fetal Thymus	thymus
32	chr3:141676200-141703800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:141676800-141688400	Weak transcription	Fetal Kidney	kidney
34	chr3:141677400-141696200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:141677800-141691200	Weak transcription	Brain Anterior Caudate	brain
36	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
37	chr3:141678200-141688600	Weak transcription	Primary B cells from cord blood	blood
38	chr3:141678600-141688600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:141679400-141690600	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:141679600-141697000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:141679800-141691400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:141680000-141686600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:141680000-141690600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:141680000-141697800	Weak transcription	NH-A	brain
46	chr3:141680000-141711200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
48	chr3:141680200-141697600	Weak transcription	Osteobl	bone
49	chr3:141680400-141697600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:141680600-141690000	Weak transcription	NHLF	lung

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