Variant report

Variant	rs3804663
Chromosome Location	chr3:145810603-145810604
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:145810601-145811128	U87	brain:	n/a	n/a
2	POLR2A	chr3:145810012-145811198	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:145808540..145810799-chr3:145816596..145819414,2	MCF-7	breast:
2	chr3:145809706..145813373-chr3:145877406..145880433,4	MCF-7	breast:
3	chr3:145795852..145797776-chr3:145810151..145811741,2	K562	blood:
4	chr3:145810461..145813616-chr3:145877675..145880858,5	MCF-7	breast:
5	chr3:145809568..145811317-chr3:145820795..145823225,2	MCF-7	breast:

No data

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

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10935601	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10935602	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10935604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1170389	0.82[JPT][hapmap]
rs1170390	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs11717610	0.81[EUR][1000 genomes]
rs12485283	0.88[JPT][hapmap]
rs12492656	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13087364	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13088180	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375580	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1375591	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1449443	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449446	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16857897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857919	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1913186	0.82[JPT][hapmap]
rs1982382	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2175668	0.82[JPT][hapmap]
rs3762694	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792340	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792345	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804667	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4611785	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681293	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681297	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56686359	0.81[EUR][1000 genomes]
rs6771106	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771118	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775684	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6781300	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6783926	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6792464	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6794727	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613150	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs7628805	1.00[JPT][hapmap]
rs7642940	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9820945	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9836725	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9869137	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
3	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
4	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
6	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
8	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
9	chr3:145784000-145811800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:145789800-145811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:145790200-145818600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:145790200-145819400	Weak transcription	Left Ventricle	heart
17	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
18	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
19	chr3:145792200-145812200	Strong transcription	HSMM	muscle
20	chr3:145794400-145811000	Weak transcription	Adipose Nuclei	Adipose
21	chr3:145794400-145815600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:145794400-145818200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:145794400-145818800	Weak transcription	Ovary	ovary
24	chr3:145794400-145827000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:145794400-145828000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:145794600-145819200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:145796200-145821400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:145798000-145818400	Weak transcription	HSMMtube	muscle
29	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:145804000-145819200	Weak transcription	NH-A	brain
31	chr3:145804400-145811800	Weak transcription	Fetal Heart	heart
32	chr3:145804600-145818000	Weak transcription	Fetal Intestine Large	intestine
33	chr3:145808400-145812400	Enhancers	Liver	Liver
34	chr3:145808600-145812000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:145808600-145833000	Weak transcription	Fetal Lung	lung
36	chr3:145808800-145811400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:145809000-145818200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:145809200-145821600	Weak transcription	HMEC	breast
39	chr3:145809600-145817200	Weak transcription	Fetal Intestine Small	intestine
40	chr3:145809800-145812200	Enhancers	A549	lung
41	chr3:145809800-145812200	Enhancers	HepG2	liver
42	chr3:145810000-145811200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr3:145810200-145812200	Genic enhancers	HUVEC	blood vessel
44	chr3:145810200-145823400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:145810400-145811800	Genic enhancers	Osteobl	bone
46	chr3:145810400-145816400	Weak transcription	Brain Substantia Nigra	brain
47	chr3:145810400-145817800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:145810400-145829000	Weak transcription	NHLF	lung
49	chr3:145810400-145830800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links