Variant report

Variant	rs7373142
Chromosome Location	chr3:139082241-139082242
allele	C/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	chr3:139082137-139082280	ProgFib	skin:	n/a	n/a
2	POLR2A	chr3:139081685-139082295	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:139082173-139082388	K562	blood:	n/a	n/a
4	POLR2A	chr3:139081681-139082830	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:139061929..139064555-chr3:139081037..139083166,2	MCF-7	breast:
2	chr3:139081658..139083880-chr3:139085722..139088665,3	MCF-7	breast:
3	chr3:139077596..139079599-chr3:139081298..139082804,2	K562	blood:

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

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1007079	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919679	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1602627	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182409	0.91[AMR][1000 genomes]
rs188419	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs192688	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs211581	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs211584	0.91[AMR][1000 genomes]
rs2233817	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278577	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295475	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs295476	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs295477	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3772874	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3772875	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821546	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60082560	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60961550	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6439863	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6776315	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72986799	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7373302	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648636	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9819224	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858740	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859683	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879736	0.91[AMR][1000 genomes]
rs9879748	0.91[AMR][1000 genomes]
rs9882253	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
3	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
4	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
5	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
6	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:139065000-139103800	Strong transcription	HSMM	muscle
8	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:139065400-139102600	Strong transcription	Osteobl	bone
20	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
22	chr3:139065600-139100200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:139065600-139101800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:139065600-139102400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:139065600-139102400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:139065600-139102400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:139065600-139103600	Strong transcription	HUVEC	blood vessel
28	chr3:139065600-139103600	Strong transcription	NH-A	brain
29	chr3:139065600-139103800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:139065600-139103800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:139065800-139095000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:139065800-139096200	Strong transcription	Liver	Liver
33	chr3:139065800-139098200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr3:139065800-139098200	Strong transcription	HMEC	breast
35	chr3:139065800-139101600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:139065800-139101600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr3:139065800-139102400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:139065800-139102400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:139065800-139102600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:139065800-139102800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:139065800-139103200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr3:139065800-139103600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:139065800-139104400	Strong transcription	Dnd41	blood
44	chr3:139066000-139084400	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:139066000-139098200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:139066000-139098200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:139066000-139101800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:139066000-139103600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr3:139066200-139099600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:139066200-139102400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links