Variant report

Variant	esv3379747
Chromosome Location	chr3:155223508-155227806
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	GATA3	chr3:155223734-155223934	SH-SY5Y	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC104472.1-1	chr3:155225371-155227121	l_2507_chr3:155225370-155321814_brain

Variant related genes	Relation type
PLCH1	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:72 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs115915305	chr3:155223515-155223516	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs550740439	chr3:155223517-155223518	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs60945017	chr3:155223538-155223539	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs549631003	chr3:155223588-155223589	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs373406095	chr3:155223591-155223592	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs34050852	chr3:155223637-155223638	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs151146236	chr3:155223664-155223665	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs545714401	chr3:155223680-155223681	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs140681514	chr3:155223681-155223682	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs75663584	chr3:155223683-155223684	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs572402279	chr3:155223685-155223686	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs78624736	chr3:155223696-155223697	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs536550183	chr3:155223737-155223738	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs547582789	chr3:155223748-155223749	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs187995451	chr3:155223778-155223779	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs576372911	chr3:155223795-155223796	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs115514450	chr3:155223830-155223831	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs543871282	chr3:155223835-155223836	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs140046012	chr3:155223868-155223869	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs112521761	chr3:155223877-155223878	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs577303130	chr3:155223894-155223895	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs191884136	chr3:155223908-155223909	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs560439473	chr3:155223914-155223915	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs527539407	chr3:155223937-155223938	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs542955631	chr3:155223942-155223943	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs114385844	chr3:155223947-155223948	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs113320694	chr3:155223948-155223949	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs66977664	chr3:155223977-155223978	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs572239868	chr3:155223979-155223980	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs80000273	chr3:155224013-155224014	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs549781069	chr3:155224063-155224064	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs571243188	chr3:155224067-155224068	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs184225840	chr3:155224080-155224081	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs115223535	chr3:155224098-155224099	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs547539272	chr3:155224101-155224102	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs564384768	chr3:155224110-155224111	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs565940841	chr3:155224124-155224125	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs57746252	chr3:155224135-155224136	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs77404024	chr3:155224137-155224138	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs111327710	chr3:155224162-155224163	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs554987618	chr3:155224206-155224207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs570356662	chr3:155224219-155224220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs537035854	chr3:155224230-155224231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs558949887	chr3:155224241-155224242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs370242164	chr3:155224262-155224263	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs187347154	chr3:155224298-155224299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs113348369	chr3:155224697-155224698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs200294708	chr3:155225314-155225315	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs201431514	chr3:155226050-155226051	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs376422474	chr3:155226313-155226314	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

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
head and neck squamous cell carcinoma	17671120	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
Breast cancer	21364760	CNVD
Basal cell lymphoma	17170743	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	22521361	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Cancer	17440070	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155195000-155230400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:155196200-155231600	Weak transcription	Gastric	stomach
3	chr3:155198400-155230600	Weak transcription	Fetal Intestine Large	intestine
4	chr3:155198800-155230800	Weak transcription	Pancreas	Pancrea
5	chr3:155199000-155229800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:155200600-155230200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:155200800-155223600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:155200800-155251400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:155202400-155230000	Weak transcription	A549	lung
10	chr3:155206800-155224000	Strong transcription	Dnd41	blood
11	chr3:155208000-155230200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:155210800-155237600	Weak transcription	Fetal Kidney	kidney
13	chr3:155212800-155230000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:155215000-155230200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:155215000-155230200	Weak transcription	Fetal Intestine Small	intestine
16	chr3:155216600-155230200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:155217400-155230000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:155218600-155229800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:155218600-155230000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:155218600-155230000	Weak transcription	Thymus	Thymus
21	chr3:155218600-155236600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:155222200-155229800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:155222400-155229800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:155222800-155230000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:155222800-155230000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:155222800-155230200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:155223200-155230200	Weak transcription	Fetal Thymus	thymus
28	chr3:155223400-155224200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:155223600-155230000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:155224000-155229800	Weak transcription	Dnd41	blood
31	chr3:155224200-155230000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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