Variant report

Variant	rs12286542
Chromosome Location	chr11:58407262-58407263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:58385876..58387982-chr11:58406021..58408836,2	MCF-7	breast:
2	chr11:58344813..58346955-chr11:58405857..58408185,2	MCF-7	breast:
3	chr11:58402145..58403700-chr11:58406157..58408220,2	K562	blood:
4	chr11:58405749..58408727-chr11:58417141..58419096,2	K562	blood:
5	chr11:58402930..58405768-chr11:58406418..58410060,3	K562	blood:

Variant related genes	Relation type
ENSG00000110031	Chromatin interaction
ENSG00000255073	Chromatin interaction
ENSG00000186660	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11229466	1.00[AFR][1000 genomes]
rs11229520	1.00[AFR][1000 genomes]
rs11229525	1.00[AFR][1000 genomes]
rs11229539	1.00[AFR][1000 genomes]
rs11229570	1.00[AFR][1000 genomes]
rs11229571	1.00[AFR][1000 genomes]
rs12271331	0.89[AFR][1000 genomes]
rs12272722	1.00[AFR][1000 genomes]
rs12278099	0.90[AFR][1000 genomes]
rs12281441	1.00[AFR][1000 genomes]
rs12282241	0.89[AFR][1000 genomes]
rs12285076	1.00[AFR][1000 genomes]
rs12293904	0.89[AFR][1000 genomes]
rs12295771	1.00[AFR][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	nsv832168	chr11:58394060-58564651	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1050444	chr11:58404467-58434568	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58393800-58407800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:58394000-58407800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:58394800-58408200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr11:58395800-58407800	Weak transcription	Fetal Thymus	thymus
5	chr11:58402400-58407800	Weak transcription	Fetal Intestine Small	intestine
6	chr11:58404400-58408000	Weak transcription	Ovary	ovary
7	chr11:58405200-58407800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:58406000-58407600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:58406000-58410200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:58406200-58408200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:58406200-58411200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:58406200-58413000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:58406600-58409200	Enhancers	Brain Hippocampus Middle	brain
14	chr11:58406800-58409000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr11:58407000-58407400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr11:58407000-58408200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:58407000-58408400	Enhancers	Brain Anterior Caudate	brain
18	chr11:58407000-58408800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr11:58407000-58408800	Enhancers	Brain Angular Gyrus	brain
20	chr11:58407000-58408800	Enhancers	Thymus	Thymus
21	chr11:58407000-58409000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr11:58407000-58409000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr11:58407000-58409000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr11:58407000-58409000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr11:58407000-58409000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:58407000-58409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:58407200-58407800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:58407200-58408400	Enhancers	Primary T cells from cord blood	blood
29	chr11:58407200-58408600	Enhancers	Left Ventricle	heart
30	chr11:58407200-58408600	Enhancers	Lung	lung
31	chr11:58407200-58408800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr11:58407200-58408800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:58407200-58408800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr11:58407200-58408800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr11:58407200-58408800	Enhancers	Spleen	Spleen
36	chr11:58407200-58408800	Enhancers	Dnd41	blood
37	chr11:58407200-58409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:58407200-58409600	Enhancers	Primary hematopoietic stem cells	blood
39	chr11:58407200-58410000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links