Variant report

Variant	rs12485589
Chromosome Location	chr3:196299700-196299701
allele	G/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	STAT3	chr3:196299493-196299769	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196294018..196298226-chr3:196298515..196305050,8	MCF-7	breast:
2	chr3:196281289..196284000-chr3:196298960..196301880,2	MCF-7	breast:
3	chr3:196297371..196300315-chr3:196436019..196438475,2	K562	blood:
4	chr3:196293630..196296577-chr3:196298745..196301924,4	MCF-7	breast:

Variant related genes	Relation type
WDR53	TF binding region
ENSG00000174013	Chromatin interaction
ENSG00000185798	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11185546	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634928	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636646	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872353	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341337	0.94[EUR][1000 genomes]
rs34676641	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35827219	0.95[EUR][1000 genomes]
rs66570007	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764637	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6791472	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6808029	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648453	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs970414	0.94[AMR][1000 genomes]
rs9870529	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12485589	FBXO45	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196296400-196304400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:196296400-196304400	Weak transcription	Lung	lung
3	chr3:196296400-196311000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:196296600-196300200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:196296600-196320200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:196296800-196305800	Weak transcription	HSMM	muscle
7	chr3:196296800-196311000	Weak transcription	Placenta	Placenta
8	chr3:196296800-196316800	Weak transcription	Right Ventricle	heart
9	chr3:196297000-196304400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:196297000-196304400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:196297000-196304400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:196297000-196304400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:196297000-196304400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:196297000-196304400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:196297000-196304400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:196297000-196304400	Weak transcription	Ovary	ovary
17	chr3:196297000-196304400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:196297000-196305000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:196297000-196305000	Weak transcription	Osteobl	bone
20	chr3:196297000-196305400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:196297000-196305400	Weak transcription	HSMMtube	muscle
22	chr3:196297000-196307200	Weak transcription	Esophagus	oesophagus
23	chr3:196297000-196307200	Weak transcription	Spleen	Spleen
24	chr3:196297000-196307400	Weak transcription	Aorta	Aorta
25	chr3:196297000-196310000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:196297000-196310800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:196297000-196311000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:196297000-196311000	Weak transcription	NH-A	brain
29	chr3:196297000-196314400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:196297000-196316000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:196297000-196316200	Weak transcription	Right Atrium	heart
32	chr3:196297000-196317000	Weak transcription	NHLF	lung
33	chr3:196297000-196317800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:196297000-196318000	Weak transcription	Colonic Mucosa	Colon
35	chr3:196297000-196320400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:196297200-196300000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:196297200-196300600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:196297200-196303000	Weak transcription	Primary T cells from cord blood	blood
39	chr3:196297200-196304400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:196297200-196304400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:196297200-196304400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:196297200-196304400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:196297200-196304400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:196297200-196304400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:196297200-196304400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:196297200-196304400	Weak transcription	Fetal Intestine Large	intestine
47	chr3:196297200-196304400	Weak transcription	Fetal Stomach	stomach
48	chr3:196297200-196304400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:196297200-196304400	Weak transcription	HepG2	liver
50	chr3:196297200-196304400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links