Variant report

Variant	rs58009483
Chromosome Location	chr12:56569624-56569625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56497759..56500713-chr12:56568434..56571351,2	MCF-7	breast:
2	chr12:56568066..56569817-chr12:56570954..56573207,2	MCF-7	breast:
3	chr12:56568053..56570139-chr12:56582886..56584432,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139613	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000170515	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10129008	1.00[EUR][1000 genomes]
rs10747763	0.95[ASN][1000 genomes]
rs10876878	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171754	1.00[EUR][1000 genomes]
rs11171755	1.00[EUR][1000 genomes]
rs11171772	1.00[ASN][1000 genomes]
rs11171777	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11834728	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229022	0.95[ASN][1000 genomes]
rs12309480	1.00[EUR][1000 genomes]
rs12320265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274502	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274503	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405859	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118333	0.83[ASN][1000 genomes]
rs2271188	0.83[ASN][1000 genomes]
rs2271190	0.83[ASN][1000 genomes]
rs2463365	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629451	1.00[ASN][1000 genomes]
rs2629453	1.00[ASN][1000 genomes]
rs2695783	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695784	1.00[ASN][1000 genomes]
rs28676339	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930788	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950573	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759096	0.83[ASN][1000 genomes]
rs3802996	0.83[ASN][1000 genomes]
rs3809130	0.83[ASN][1000 genomes]
rs4759218	0.95[ASN][1000 genomes]
rs55887836	1.00[EUR][1000 genomes]
rs56851901	0.83[ASN][1000 genomes]
rs57280585	0.83[ASN][1000 genomes]
rs57822276	0.83[ASN][1000 genomes]
rs58476735	0.83[ASN][1000 genomes]
rs58548156	0.83[ASN][1000 genomes]
rs58663297	0.83[ASN][1000 genomes]
rs59053322	1.00[ASN][1000 genomes]
rs59078852	1.00[ASN][1000 genomes]
rs59420211	1.00[EUR][1000 genomes]
rs59966703	1.00[ASN][1000 genomes]
rs60396934	0.83[ASN][1000 genomes]
rs61939011	1.00[ASN][1000 genomes]
rs6581091	0.95[ASN][1000 genomes]
rs703823	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311008	0.95[ASN][1000 genomes]
rs73340401	1.00[EUR][1000 genomes]
rs74092003	1.00[EUR][1000 genomes]
rs7489249	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773654	1.00[ASN][1000 genomes]
rs773655	0.90[ASN][1000 genomes]
rs773658	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773659	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773660	0.90[ASN][1000 genomes]
rs773661	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956599	0.81[ASN][1000 genomes]
rs7956926	0.81[ASN][1000 genomes]
rs7962107	1.00[ASN][1000 genomes]
rs7967464	1.00[ASN][1000 genomes]
rs7975405	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 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	chr12:56554000-56582000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56554200-56581400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56555000-56575600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:56555000-56579800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:56555000-56580800	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr12:56555000-56580800	Strong transcription	Brain Anterior Caudate	brain
7	chr12:56555000-56581000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:56555200-56573600	Strong transcription	Fetal Lung	lung
9	chr12:56555200-56578800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:56555200-56580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:56555200-56580800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:56555400-56579000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:56555400-56580000	Strong transcription	Placenta	Placenta
14	chr12:56555400-56580600	Strong transcription	Thymus	Thymus
15	chr12:56555400-56580800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:56555400-56580800	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr12:56555400-56580800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:56555600-56573600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr12:56555600-56575400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:56555600-56576000	Strong transcription	Brain Cingulate Gyrus	brain
21	chr12:56555600-56580600	Strong transcription	Fetal Brain Female	brain
22	chr12:56555600-56580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:56555600-56580800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:56555600-56580800	Strong transcription	Liver	Liver
25	chr12:56555600-56580800	Strong transcription	Osteobl	bone
26	chr12:56555800-56573400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr12:56555800-56580200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:56555800-56580600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:56555800-56580600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:56555800-56580800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:56555800-56580800	Strong transcription	Fetal Thymus	thymus
32	chr12:56555800-56580800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:56555800-56581000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:56556000-56573400	Strong transcription	GM12878-XiMat	blood
35	chr12:56556000-56573400	Strong transcription	NHEK	skin
36	chr12:56556000-56573600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr12:56556000-56578000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:56556000-56580800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:56556000-56580800	Strong transcription	Fetal Intestine Large	intestine
40	chr12:56556000-56581000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:56556000-56581000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:56556200-56574600	Strong transcription	Fetal Intestine Small	intestine
43	chr12:56556400-56573400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:56556400-56580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:56556400-56580400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:56556600-56579800	Strong transcription	Dnd41	blood
47	chr12:56556600-56580600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:56556600-56580600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr12:56556600-56580800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:56556600-56581000	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links