Variant report

Variant	nsv963527
Chromosome Location	chr3:105259211-105267049
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	chr3:105261964-105262123	GM12878	blood:	n/a	n/a
2	CTCF	chr3:105262006-105262077	Spleen_OC	spleen:	n/a	n/a
3	MAFK	chr3:105263754-105263781	HepG2	liver:	n/a	n/a
4	MAZ	chr3:105266605-105266805	HepG2	liver:	n/a	n/a
5	MYC	chr3:105261258-105261369	MCF10A-Er-Src	breast:	n/a	n/a
6	NRF1	chr3:105263891-105263914	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:105263535-105263657	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr3:105264096-105264227	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr3:105260904-105261085	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr3:105259222-105259378	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105259203..105260884-chr3:105262936..105265774,2	MCF-7	breast:

Variant related genes	Relation type
ALCAM	TF binding region
ENSG00000170017	chromatin interactions

Extended variants
information (count: 296 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:296 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs559962552	chr3:105259281-105259282	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs76083733	chr3:105259300-105259301	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs2279389	chr3:105259312-105259313	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs187178841	chr3:105259341-105259342	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs542417169	chr3:105259393-105259394	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs2279388	chr3:105259406-105259407	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs569098447	chr3:105259439-105259440	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs192485163	chr3:105259445-105259446	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs557850763	chr3:105259490-105259491	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs566452286	chr3:105259525-105259526	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs533733890	chr3:105259537-105259538	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs555115317	chr3:105259605-105259606	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs575067959	chr3:105259740-105259741	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs561562581	chr3:105259764-105259765	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs139278312	chr3:105259794-105259795	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs557111551	chr3:105259795-105259796	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs528871512	chr3:105259800-105259801	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs550307105	chr3:105259805-105259806	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs575406979	chr3:105259825-105259826	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs182404501	chr3:105259872-105259873	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs73854324	chr3:105259875-105259876	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs114939405	chr3:105259915-105259916	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs540621621	chr3:105259948-105259949	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs145426784	chr3:105259949-105259950	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs3836274	chr3:105259960-105259961	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs561983639	chr3:105259967-105259968	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs529178117	chr3:105259972-105259973	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs550863911	chr3:105260035-105260036	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs149397767	chr3:105260057-105260058	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs143844184	chr3:105260091-105260092	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs551603481	chr3:105260112-105260113	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs566778280	chr3:105260162-105260163	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs78233624	chr3:105260222-105260223	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs112779326	chr3:105260257-105260258	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs113877143	chr3:105260271-105260272	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs533690032	chr3:105260275-105260276	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs548948813	chr3:105260340-105260341	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs567178899	chr3:105260369-105260370	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs141977510	chr3:105260381-105260382	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs557199448	chr3:105260401-105260402	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs112413104	chr3:105260419-105260420	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs186869176	chr3:105260436-105260437	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs190097721	chr3:105260437-105260438	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs369105011	chr3:105260503-105260504	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs558118117	chr3:105260515-105260516	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs579565	chr3:105260518-105260519	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs1044243	chr3:105260520-105260521	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs377544425	chr3:105260521-105260522	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs199921428	chr3:105260522-105260523	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs35271455	chr3:105260524-105260525	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	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:202 , 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	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
3	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
7	chr3:105234200-105260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:105234600-105260600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:105241000-105260400	Weak transcription	Pancreas	Pancrea
14	chr3:105241600-105260200	Weak transcription	HepG2	liver
15	chr3:105242000-105259800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:105242000-105293600	Weak transcription	Lung	lung
17	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:105245600-105260400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:105245800-105260600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:105245800-105268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:105247400-105260400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:105248000-105281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:105248200-105262800	Weak transcription	NHLF	lung
27	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:105249400-105278600	Weak transcription	Small Intestine	intestine
29	chr3:105249800-105261200	Weak transcription	Fetal Intestine Small	intestine
30	chr3:105249800-105263400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
32	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:105250600-105262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:105250600-105270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:105251200-105266400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:105251800-105274400	Weak transcription	Dnd41	blood
37	chr3:105252600-105263400	Weak transcription	Left Ventricle	heart
38	chr3:105253000-105259400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:105253200-105273000	Weak transcription	Gastric	stomach
40	chr3:105253600-105260400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:105253600-105260400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:105253800-105259400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:105253800-105260400	Weak transcription	Aorta	Aorta
44	chr3:105253800-105270000	Weak transcription	Fetal Intestine Large	intestine
45	chr3:105254000-105273000	Weak transcription	Fetal Lung	lung
46	chr3:105254800-105279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:105255800-105260400	Weak transcription	HSMM	muscle
48	chr3:105256200-105268200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:105256400-105260600	Weak transcription	NHEK	skin
50	chr3:105256600-105259400	Weak transcription	Brain Hippocampus Middle	brain

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