Variant report

Variant	rs12721590
Chromosome Location	chr12:57499432-57499433
allele	A/C/G
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	chr12:57499281-57499563	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:57499175-57499619	K562	blood:	n/a	n/a
3	POLR2A	chr12:57497767-57502742	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:57499210-57499994	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:57499416-57499537	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:57499354-57499981	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
STAT6	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10467125	0.96[ASN][1000 genomes]
rs11172112	0.96[ASN][1000 genomes]
rs12307379	0.96[ASN][1000 genomes]
rs2270735	1.00[AFR][1000 genomes]
rs3024948	1.00[ASN][1000 genomes]
rs3024950	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3024961	0.82[ASN][1000 genomes]
rs3024963	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36234207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36234211	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306742	0.96[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57486200-57503600	Weak transcription	Fetal Brain Male	brain
2	chr12:57486600-57503800	Weak transcription	Brain Substantia Nigra	brain
3	chr12:57487600-57501400	Weak transcription	Right Atrium	heart
4	chr12:57487600-57503600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:57488800-57501400	Strong transcription	Adipose Nuclei	Adipose
6	chr12:57488800-57502400	Strong transcription	Fetal Stomach	stomach
7	chr12:57489000-57503600	Weak transcription	Brain Angular Gyrus	brain
8	chr12:57489400-57501400	Strong transcription	Lung	lung
9	chr12:57489400-57501600	Strong transcription	Ovary	ovary
10	chr12:57489600-57500200	Weak transcription	Fetal Kidney	kidney
11	chr12:57490000-57503800	Weak transcription	NH-A	brain
12	chr12:57490000-57504000	Weak transcription	Brain Germinal Matrix	brain
13	chr12:57490400-57503400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:57491000-57501400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:57492600-57500400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:57492800-57499600	Weak transcription	Fetal Heart	heart
17	chr12:57493000-57503200	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:57493000-57503400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:57493200-57501400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:57493200-57501400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:57493200-57501600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:57493400-57503200	Weak transcription	HUVEC	blood vessel
23	chr12:57494000-57502600	Strong transcription	Placenta	Placenta
24	chr12:57494000-57504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:57495600-57501000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:57495600-57501400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:57495600-57501600	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr12:57495800-57501200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr12:57495800-57501600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:57495800-57501800	Strong transcription	Fetal Lung	lung
31	chr12:57495800-57502600	Strong transcription	Osteobl	bone
32	chr12:57496000-57501600	Strong transcription	GM12878-XiMat	blood
33	chr12:57496000-57502400	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr12:57496400-57502200	Strong transcription	Thymus	Thymus
35	chr12:57496600-57500200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:57496600-57501600	Strong transcription	Fetal Thymus	thymus
37	chr12:57496600-57502000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:57496600-57502200	Strong transcription	Spleen	Spleen
39	chr12:57496600-57503200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:57496800-57500800	Strong transcription	Fetal Intestine Small	intestine
41	chr12:57496800-57501600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr12:57496800-57502200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:57496800-57504000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:57497200-57500600	Strong transcription	Fetal Intestine Large	intestine
45	chr12:57497400-57500000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:57497400-57501600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:57497400-57501800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr12:57497400-57502000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:57497400-57502600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:57497400-57502600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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