Variant report

Variant	rs2541134
Chromosome Location	chr12:11803354-11803355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:11800455..11804262-chr12:12036773..12041762,7	MCF-7	breast:
2	chr12:11803344..11805107-chr12:11973209..11975681,2	MCF-7	breast:
3	chr12:11800191..11804184-chr12:12034563..12039946,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11833038	1.00[AMR][1000 genomes]
rs1861485	1.00[AMR][1000 genomes]
rs2541120	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2541136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2724591	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2724607	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2724647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2856312	1.00[AMR][1000 genomes]
rs2856318	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7302827	1.00[JPT][hapmap]

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	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11801000-11804000	Active TSS	Rectal Mucosa Donor 31	rectum
2	chr12:11801000-11804600	Active TSS	Fetal Kidney	kidney
3	chr12:11801000-11804800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:11801000-11805200	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:11801200-11803800	Active TSS	Placenta Amnion	Placenta Amnion
6	chr12:11801200-11804800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr12:11801200-11805200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:11801200-11805200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:11801200-11805200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:11801200-11805600	Active TSS	Fetal Muscle Trunk	muscle
11	chr12:11801200-11805800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:11801200-11806000	Active TSS	GM12878-XiMat	blood
13	chr12:11801400-11803600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:11801400-11803600	Active TSS	Primary T cells from cord blood	blood
15	chr12:11801400-11803600	Active TSS	HepG2	liver
16	chr12:11801400-11803800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:11801400-11803800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:11801400-11803800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:11801400-11803800	Active TSS	Fetal Lung	lung
20	chr12:11801400-11803800	Active TSS	A549	lung
21	chr12:11801400-11804000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:11801400-11804000	Active TSS	Hela-S3	cervix
23	chr12:11801400-11804000	Active TSS	HSMM	muscle
24	chr12:11801400-11804200	Active TSS	Brain Germinal Matrix	brain
25	chr12:11801400-11804200	Active TSS	Pancreas	Pancrea
26	chr12:11801400-11804200	Active TSS	HSMMtube	muscle
27	chr12:11801400-11804200	Active TSS	Osteobl	bone
28	chr12:11801400-11804400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:11801400-11804400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:11801400-11804400	Active TSS	Fetal Intestine Small	intestine
31	chr12:11801400-11804600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:11801400-11804600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:11801400-11804600	Active TSS	Duodenum Mucosa	Duodenum
34	chr12:11801400-11804800	Active TSS	Brain Cingulate Gyrus	brain
35	chr12:11801400-11804800	Active TSS	Psoas Muscle	Psoas
36	chr12:11801400-11805000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr12:11801400-11805000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:11801400-11805200	Active TSS	Brain Anterior Caudate	brain
39	chr12:11801400-11805200	Active TSS	Fetal Brain Female	brain
40	chr12:11801400-11805200	Active TSS	Fetal Intestine Large	intestine
41	chr12:11801400-11805400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:11801400-11805400	Active TSS	Brain Angular Gyrus	brain
43	chr12:11801400-11805400	Active TSS	Brain Hippocampus Middle	brain
44	chr12:11801400-11805400	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr12:11801400-11805400	Active TSS	NHLF	lung
46	chr12:11801400-11805600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr12:11801400-11805600	Active TSS	Right Atrium	heart
48	chr12:11801400-11805800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:11801400-11805800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:11801400-11805800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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