Variant report

Variant	rs58545752
Chromosome Location	chr12:4666524-4666525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:4646100..4649661-chr12:4665332..4668366,3	K562	blood:
2	chr12:4664462..4667424-chr12:4914482..4915996,2	K562	blood:
3	chr12:4651757..4653474-chr12:4666436..4667992,2	MCF-7	breast:
4	chr12:4664388..4668244-chr12:4668539..4671250,3	K562	blood:
5	chr12:4666221..4667808-chr12:4669530..4671066,2	K562	blood:
6	chr12:4660124..4662897-chr12:4666466..4668044,2	K562	blood:

Variant related genes	Relation type
ENSG00000111247	Chromatin interaction
ENSG00000047621	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11832481	0.91[AFR][1000 genomes]
rs11833007	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16931471	0.84[AFR][1000 genomes]
rs16931500	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16931505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16931512	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16931542	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57829228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60119908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61154618	0.83[AFR][1000 genomes]
rs61731955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61752088	0.83[AFR][1000 genomes]
rs6489549	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6489550	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6489551	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7956610	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7958954	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7959710	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7964538	0.91[AFR][1000 genomes]
rs7969764	1.00[AMR][1000 genomes]
rs7970305	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7970521	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974236	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1038332	chr12:4627992-4689300	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541362	chr12:4627992-4689300	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4648400-4670200	Weak transcription	Left Ventricle	heart
2	chr12:4648400-4671200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:4648400-4671400	Weak transcription	Esophagus	oesophagus
4	chr12:4648600-4671200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:4648800-4669600	Weak transcription	Fetal Brain Male	brain
6	chr12:4648800-4670800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:4648800-4671000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:4649000-4671000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:4649000-4671000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:4649000-4671000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:4649000-4671200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:4649200-4670800	Weak transcription	Fetal Intestine Small	intestine
13	chr12:4649400-4671000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:4649400-4671000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:4649400-4671000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:4649600-4671000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:4649600-4671000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:4649600-4671000	Weak transcription	Fetal Kidney	kidney
19	chr12:4649600-4671200	Weak transcription	NHEK	skin
20	chr12:4650200-4668600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:4650200-4670600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:4650400-4670000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:4650400-4670200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:4651000-4670400	Strong transcription	Fetal Thymus	thymus
25	chr12:4651200-4668200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:4651400-4666600	Strong transcription	A549	lung
27	chr12:4651600-4668400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:4652000-4671800	Strong transcription	Dnd41	blood
29	chr12:4654400-4671000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr12:4655400-4671000	Weak transcription	NH-A	brain
31	chr12:4655600-4671000	Weak transcription	Osteobl	bone
32	chr12:4656600-4668600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:4657000-4671000	Weak transcription	NHDF-Ad	bronchial
34	chr12:4657800-4671000	Weak transcription	Fetal Intestine Large	intestine
35	chr12:4658000-4671000	Weak transcription	Fetal Heart	heart
36	chr12:4658400-4671600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:4659000-4671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:4659200-4670000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:4659400-4670200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:4659400-4671200	Weak transcription	Primary T cells from cord blood	blood
41	chr12:4659800-4671000	Weak transcription	Brain Germinal Matrix	brain
42	chr12:4659800-4671000	Weak transcription	K562	blood
43	chr12:4660000-4671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:4660000-4671400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:4660200-4671000	Weak transcription	HepG2	liver
46	chr12:4660200-4671000	Weak transcription	HUVEC	blood vessel
47	chr12:4661200-4669000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:4661800-4670400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:4662000-4667200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:4662000-4671000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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