Variant report

Variant	rs67929453
Chromosome Location	chr3:139109825-139109826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr3:139109440-139109957	K562	blood:	n/a	n/a
2	POLR2A	chr3:139107767-139110035	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:139106214-139110153	IMR90	lung:	n/a	n/a
4	RPC155	chr3:139109037-139109894	K562	blood:	n/a	n/a
5	POLR2A	chr3:139109825-139110506	MCF10A-Er-Src	breast:	n/a	n/a
6	RPC155	chr3:139109001-139109868	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:139107677-139110513	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:139108349..139110080-chr3:140659758..140661262,2	MCF-7	breast:
2	chr3:139109720..139111742-chr3:139198602..139200666,2	K562	blood:
3	chr3:139061660..139066893-chr3:139105523..139110764,11	K562	blood:
4	chr3:139088868..139091914-chr3:139107086..139109851,3	K562	blood:
5	chr3:139063205..139066777-chr3:139105523..139110764,7	K562	blood:

No data

Variant related genes	Relation type
COPB2	TF binding region
ENSG00000114113	Chromatin interaction
ENSG00000175110	Chromatin interaction
ENSG00000184432	Chromatin interaction
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1044826	0.92[ASN][1000 genomes]
rs10460845	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10935320	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935323	0.98[ASN][1000 genomes]
rs12488939	0.86[ASN][1000 genomes]
rs12494556	0.81[ASN][1000 genomes]
rs12494806	0.95[ASN][1000 genomes]
rs12695698	0.90[ASN][1000 genomes]
rs12695699	0.90[ASN][1000 genomes]
rs12695700	0.82[ASN][1000 genomes]
rs13060697	0.93[ASN][1000 genomes]
rs13074208	0.82[ASN][1000 genomes]
rs13083195	0.90[ASN][1000 genomes]
rs13085888	0.88[ASN][1000 genomes]
rs13086868	0.81[ASN][1000 genomes]
rs13089007	0.98[ASN][1000 genomes]
rs13089052	0.81[ASN][1000 genomes]
rs13089090	0.87[ASN][1000 genomes]
rs13092507	0.85[ASN][1000 genomes]
rs13092935	0.90[ASN][1000 genomes]
rs1586861	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1586863	0.92[ASN][1000 genomes]
rs1586864	0.92[ASN][1000 genomes]
rs17336869	0.92[ASN][1000 genomes]
rs1907687	0.92[ASN][1000 genomes]
rs2165139	0.82[ASN][1000 genomes]
rs2233811	0.92[ASN][1000 genomes]
rs2233815	0.92[ASN][1000 genomes]
rs2349059	0.88[ASN][1000 genomes]
rs34623690	0.92[ASN][1000 genomes]
rs3772877	0.93[ASN][1000 genomes]
rs3772878	0.93[ASN][1000 genomes]
rs3772879	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821544	0.92[ASN][1000 genomes]
rs3821545	0.93[ASN][1000 genomes]
rs4544576	0.92[ASN][1000 genomes]
rs4683818	0.81[ASN][1000 genomes]
rs747346	0.81[ASN][1000 genomes]
rs9289578	0.92[ASN][1000 genomes]
rs964227	0.88[ASN][1000 genomes]
rs973691	0.92[ASN][1000 genomes]
rs9812192	0.92[ASN][1000 genomes]
rs9818691	0.95[ASN][1000 genomes]
rs9825064	0.86[ASN][1000 genomes]
rs9831108	0.98[ASN][1000 genomes]
rs9834607	0.82[ASN][1000 genomes]
rs9835241	0.82[ASN][1000 genomes]
rs9848241	0.92[ASN][1000 genomes]
rs9849039	0.88[ASN][1000 genomes]
rs9849578	0.98[ASN][1000 genomes]
rs9853350	0.98[ASN][1000 genomes]
rs9860201	0.98[ASN][1000 genomes]
rs9860521	0.82[ASN][1000 genomes]
rs9868544	0.88[ASN][1000 genomes]
rs9882014	0.90[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139106600-139110400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr3:139106800-139110000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:139107000-139110200	Active TSS	A549	lung
4	chr3:139107200-139110200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:139107400-139110000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:139107400-139110000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:139107400-139110000	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr3:139109200-139110200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:139109200-139110200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr3:139109200-139123400	Weak transcription	Lung	lung
11	chr3:139109400-139110000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:139109400-139110000	Weak transcription	Brain Substantia Nigra	brain
13	chr3:139109400-139110600	Enhancers	Fetal Heart	heart
14	chr3:139109400-139110600	Enhancers	Fetal Lung	lung
15	chr3:139109400-139110800	Enhancers	Left Ventricle	heart
16	chr3:139109400-139123400	Weak transcription	Aorta	Aorta
17	chr3:139109600-139110000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:139109600-139110000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:139109600-139110200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:139109600-139110200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr3:139109600-139110400	Enhancers	Fetal Kidney	kidney
22	chr3:139109600-139110400	Flanking Active TSS	HepG2	liver
23	chr3:139109600-139110600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:139109600-139110600	Enhancers	Liver	Liver
25	chr3:139109600-139110600	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:139109600-139111000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:139109600-139111000	Enhancers	Fetal Intestine Large	intestine
28	chr3:139109600-139112800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:139109600-139118000	Weak transcription	Brain Angular Gyrus	brain
30	chr3:139109600-139123400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:139109800-139110000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:139109800-139110000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:139109800-139110000	Flanking Active TSS	Hela-S3	cervix
34	chr3:139109800-139110000	Active TSS	K562	blood
35	chr3:139109800-139110000	Enhancers	NHEK	skin
36	chr3:139109800-139110000	Enhancers	Osteobl	bone
37	chr3:139109800-139110200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:139109800-139110200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:139109800-139110200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:139109800-139110200	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:139109800-139110200	Enhancers	Fetal Intestine Small	intestine
42	chr3:139109800-139110200	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr3:139109800-139110200	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr3:139109800-139110400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:139109800-139110400	Enhancers	GM12878-XiMat	blood
46	chr3:139109800-139110400	Enhancers	NHDF-Ad	bronchial
47	chr3:139109800-139110600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:139109800-139110600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:139109800-139110600	Enhancers	Colon Smooth Muscle	Colon
50	chr3:139109800-139110600	Enhancers	Skeletal Muscle Male	skeletal muscle

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