Variant report

Variant	rs3762694
Chromosome Location	chr3:145790519-145790520
allele	A/T
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	POLR2A	chr3:145788381-145790538	U87	brain:	n/a	n/a
2	POLR2A	chr3:145788406-145790532	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145787365..145792721-chr3:145875341..145880381,7	MCF-7	breast:

Variant related genes	Relation type
PLOD2	TF binding region
ENSG00000240032	TF binding region
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10935601	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10935602	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10935604	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1170390	0.84[EUR][1000 genomes]
rs11717610	0.81[EUR][1000 genomes]
rs12492656	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13087364	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13088180	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375580	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1375591	0.84[EUR][1000 genomes]
rs1449443	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449446	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16857897	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857919	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1982382	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792340	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804663	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804667	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4611785	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681293	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681297	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56686359	0.81[EUR][1000 genomes]
rs6771106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771118	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775684	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6781300	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6783926	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6792464	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6794727	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613150	0.82[EUR][1000 genomes]
rs7642940	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9820945	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9836725	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9869137	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv965397	chr3:145789376-145797057	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145774600-145795400	Weak transcription	Aorta	Aorta
2	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
4	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
5	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
7	chr3:145780800-145793800	Weak transcription	Ovary	ovary
8	chr3:145780800-145793800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
11	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
12	chr3:145784000-145811800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:145784800-145794000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:145785200-145806400	Weak transcription	Colonic Mucosa	Colon
16	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:145785400-145791800	Strong transcription	HSMM	muscle
18	chr3:145785400-145796800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:145785600-145790800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr3:145785600-145790800	Weak transcription	NHDF-Ad	bronchial
21	chr3:145785600-145798600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:145786000-145790800	Strong transcription	HUVEC	blood vessel
23	chr3:145786400-145791000	Genic enhancers	A549	lung
24	chr3:145786600-145792800	Strong transcription	HepG2	liver
25	chr3:145786800-145793800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:145787000-145807200	Weak transcription	Fetal Lung	lung
27	chr3:145787200-145798400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:145787400-145793200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:145787400-145793800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:145787600-145798200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:145787800-145791200	Weak transcription	Small Intestine	intestine
32	chr3:145788400-145791000	Strong transcription	NH-A	brain
33	chr3:145788400-145793000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:145789000-145791000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:145789200-145790600	Enhancers	Adipose Nuclei	Adipose
36	chr3:145789200-145791000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:145789200-145796000	Weak transcription	HMEC	breast
38	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:145789400-145791200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:145789400-145793800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:145789600-145790800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:145789600-145791800	Enhancers	Fetal Heart	heart
43	chr3:145789600-145793800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:145789800-145791000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:145789800-145793800	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:145789800-145811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:145790000-145791600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:145790000-145791800	Genic enhancers	Osteobl	bone
49	chr3:145790000-145808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links