Variant report

Variant	rs12297092
Chromosome Location	chr12:117594861-117594862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117593960..117595823-chr12:117626957..117629647,2	MCF-7	breast:
2	chr12:117591837..117594892-chr12:117625944..117630228,6	K562	blood:
3	chr12:117587735..117590718-chr12:117591687..117594987,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135108	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1060233	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10850778	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10850779	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850780	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068380	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068388	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11068393	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12298285	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12316322	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319767	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12322862	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17508240	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4238052	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4766832	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766833	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4767508	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4767509	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767510	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4767517	0.82[EUR][1000 genomes]
rs56014034	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61568898	0.85[ASN][1000 genomes]
rs73206036	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73206082	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7487508	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats 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	nsv899542	chr12:117549739-117623136	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117572400-117596000	Weak transcription	Fetal Brain Male	brain
2	chr12:117578200-117617200	Strong transcription	Fetal Stomach	stomach
3	chr12:117579000-117618200	Strong transcription	Thymus	Thymus
4	chr12:117579200-117602600	Weak transcription	Psoas Muscle	Psoas
5	chr12:117579200-117623000	Strong transcription	Primary T cells from cord blood	blood
6	chr12:117579400-117616800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:117580000-117625000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr12:117580000-117626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:117580400-117618800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:117580600-117625600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:117581200-117618400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr12:117581200-117624600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr12:117581400-117624200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:117581400-117625800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:117581600-117618800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:117582000-117613200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:117582200-117606200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:117582200-117623400	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr12:117582200-117625800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:117582400-117624400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:117582600-117608400	Strong transcription	Liver	Liver
22	chr12:117584000-117595400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:117585600-117619000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:117585600-117619800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:117585800-117600600	Strong transcription	Primary B cells from cord blood	blood
26	chr12:117585800-117602800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:117585800-117625600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:117586800-117596000	Strong transcription	Hela-S3	cervix
29	chr12:117588800-117618800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:117588800-117619000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:117589400-117604000	Weak transcription	Fetal Heart	heart
32	chr12:117589400-117623600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:117589600-117614600	Strong transcription	Lung	lung
34	chr12:117589600-117619400	Strong transcription	Brain Germinal Matrix	brain
35	chr12:117589800-117601000	Strong transcription	Brain Angular Gyrus	brain
36	chr12:117589800-117618800	Strong transcription	Fetal Brain Female	brain
37	chr12:117590000-117595600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:117590000-117596000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:117590000-117599000	Weak transcription	Stomach Mucosa	stomach
40	chr12:117590000-117602400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:117590000-117626200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:117590200-117600600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:117590200-117618800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr12:117590200-117626800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:117590600-117599000	Strong transcription	Ovary	ovary
46	chr12:117590600-117602800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr12:117590600-117606200	Strong transcription	Colonic Mucosa	Colon
48	chr12:117590600-117616600	Strong transcription	Fetal Muscle Leg	muscle
49	chr12:117590600-117618200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:117590600-117618400	Strong transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links