Variant report

Variant	nsv1008291
Chromosome Location	chr3:105261480-105272449
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	CTCF	chr3:105271760-105271910	MCF-7	breast:	n/a	n/a
2	CTCF	chr3:105267347-105267430	Kidney_OC	kidney:	n/a	n/a
3	CTCF	chr3:105262006-105262077	Spleen_OC	spleen:	n/a	n/a
4	CTCF	chr3:105261964-105262123	GM12878	blood:	n/a	n/a
5	CTCF	chr3:105271782-105271863	MCF-7	breast:	n/a	n/a
6	CUX1	chr3:105270200-105270213	K562	blood:	n/a	n/a
7	MAFK	chr3:105263754-105263781	HepG2	liver:	n/a	n/a
8	MAFK	chr3:105267951-105268107	HepG2	liver:	n/a	n/a
9	MAZ	chr3:105266605-105266805	HepG2	liver:	n/a	n/a
10	NRF1	chr3:105263891-105263914	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:105263535-105263657	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr3:105264096-105264227	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105272104..105273978-chr3:105278309..105280782,2	MCF-7	breast:

Variant related genes	Relation type
ALCAM	TF binding region

Extended variants
information (count: 411 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:411 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3772550	chr3:105261480-105261481	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs551750637	chr3:105261498-105261499	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs540608549	chr3:105261590-105261591	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs535745179	chr3:105261597-105261598	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs185446422	chr3:105261600-105261601	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs555972488	chr3:105261636-105261637	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs567752484	chr3:105261658-105261659	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs375295447	chr3:105261662-105261663	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs562401436	chr3:105261687-105261688	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs77393373	chr3:105261690-105261691	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs78682389	chr3:105261725-105261726	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs583889	chr3:105261753-105261754	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs545401138	chr3:105261761-105261762	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs543763186	chr3:105261792-105261793	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs553744486	chr3:105261815-105261816	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs148481847	chr3:105261840-105261841	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs188614231	chr3:105261856-105261857	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs503321	chr3:105261887-105261888	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs531294077	chr3:105261909-105261910	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs543144038	chr3:105261959-105261960	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs564651784	chr3:105261960-105261961	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs193256042	chr3:105261974-105261975	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs374611349	chr3:105261980-105261981	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs183528116	chr3:105261982-105261983	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs79561068	chr3:105262005-105262006	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs138470677	chr3:105262006-105262007	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs551043214	chr3:105262049-105262050	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs28527180	chr3:105262053-105262054	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs526297	chr3:105262148-105262149	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs528027113	chr3:105262191-105262192	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs527474411	chr3:105262197-105262198	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs567886114	chr3:105262204-105262205	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs538463102	chr3:105262214-105262215	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs556660846	chr3:105262254-105262255	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs571724225	chr3:105262283-105262284	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs549057037	chr3:105262364-105262365	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs538611107	chr3:105262365-105262366	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs554186712	chr3:105262366-105262367	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs572244099	chr3:105262367-105262368	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs542944660	chr3:105262370-105262371	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs188216013	chr3:105262389-105262390	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs3836273	chr3:105262401-105262402	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs147671308	chr3:105262414-105262415	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs142334030	chr3:105262416-105262417	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs553737615	chr3:105262467-105262468	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs576916797	chr3:105262530-105262531	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs180971854	chr3:105262536-105262537	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs573868900	chr3:105262548-105262549	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs535861131	chr3:105262552-105262553	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs146606361	chr3:105262558-105262559	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
Renal cell carcinoma	21668985	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
small cell lung cancer	20016488	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
Splenic marginal zone lymphoma	21957467	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:250 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
5	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:105242000-105293600	Weak transcription	Lung	lung
9	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:105245800-105268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:105248000-105281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:105248200-105262800	Weak transcription	NHLF	lung
16	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:105249400-105278600	Weak transcription	Small Intestine	intestine
18	chr3:105249800-105263400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
20	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:105250600-105262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:105250600-105270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:105251200-105266400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:105251800-105274400	Weak transcription	Dnd41	blood
25	chr3:105252600-105263400	Weak transcription	Left Ventricle	heart
26	chr3:105253200-105273000	Weak transcription	Gastric	stomach
27	chr3:105253800-105270000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:105254000-105273000	Weak transcription	Fetal Lung	lung
29	chr3:105254800-105279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:105256200-105268200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:105257200-105269400	Weak transcription	Fetal Heart	heart
32	chr3:105257400-105272400	Weak transcription	NHDF-Ad	bronchial
33	chr3:105257800-105271400	Weak transcription	Stomach Mucosa	stomach
34	chr3:105258000-105270200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:105258000-105274600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:105258200-105263800	Strong transcription	HMEC	breast
37	chr3:105258200-105268400	Strong transcription	GM12878-XiMat	blood
38	chr3:105258600-105273600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:105258800-105264800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:105258800-105266600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:105258800-105267000	Strong transcription	Primary B cells from cord blood	blood
42	chr3:105258800-105271800	Strong transcription	HUVEC	blood vessel
43	chr3:105258800-105274400	Strong transcription	Liver	Liver
44	chr3:105258800-105274400	Strong transcription	NH-A	brain
45	chr3:105259000-105264000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:105259000-105264400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr3:105259000-105271200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:105259000-105273400	Strong transcription	Osteobl	bone
49	chr3:105259200-105261600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr3:105259200-105262000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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