Variant report

Variant	rs12426555
Chromosome Location	chr12:59302853-59302854
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59300516..59303019-chr12:59309552..59311828,2	MCF-7	breast:
2	chr12:59300890..59303291-chr12:59306995..59308864,2	MCF-7	breast:
3	chr12:59301019..59303651-chr12:59478405..59481329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139263	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10877187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172802	0.83[EUR][1000 genomes]
rs11172804	0.83[EUR][1000 genomes]
rs11172806	0.80[EUR][1000 genomes]
rs11172807	0.83[EUR][1000 genomes]
rs11172809	0.83[EUR][1000 genomes]
rs11172823	0.85[CHB][hapmap];0.85[MEX][hapmap]
rs11172824	0.85[CHB][hapmap];0.85[MEX][hapmap]
rs7967566	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
2	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:59284200-59304600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:59289800-59304600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:59289800-59305400	Weak transcription	Spleen	Spleen
7	chr12:59290600-59307200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:59290600-59311000	Weak transcription	Right Ventricle	heart
9	chr12:59292400-59309200	Weak transcription	Fetal Heart	heart
10	chr12:59292400-59310600	Weak transcription	Small Intestine	intestine
11	chr12:59292600-59303000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:59297800-59303800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr12:59297800-59305400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:59297800-59305400	Strong transcription	Liver	Liver
15	chr12:59297800-59305400	Strong transcription	Osteobl	bone
16	chr12:59297800-59306400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:59297800-59307400	Strong transcription	Fetal Intestine Large	intestine
18	chr12:59297800-59307600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr12:59297800-59307600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:59297800-59308000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:59297800-59308000	Strong transcription	NHDF-Ad	bronchial
22	chr12:59298200-59306800	Weak transcription	Fetal Brain Male	brain
23	chr12:59298400-59303600	Weak transcription	Stomach Mucosa	stomach
24	chr12:59298600-59303000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:59298600-59307800	Strong transcription	NHLF	lung
26	chr12:59299000-59303000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:59299000-59303200	Strong transcription	Fetal Intestine Small	intestine
28	chr12:59299000-59305200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:59299400-59306400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:59300000-59304800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:59300200-59305200	Genic enhancers	HMEC	breast
32	chr12:59300200-59306400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr12:59300400-59303000	Genic enhancers	Fetal Muscle Leg	muscle
34	chr12:59300400-59304800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:59300400-59307600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:59300600-59303000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:59300600-59306800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr12:59300800-59303200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:59300800-59303800	Genic enhancers	Fetal Stomach	stomach
40	chr12:59300800-59303800	Genic enhancers	Stomach Smooth Muscle	stomach
41	chr12:59300800-59307600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:59301000-59303400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:59301200-59309400	Weak transcription	GM12878-XiMat	blood
44	chr12:59301400-59304400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:59301400-59306400	Strong transcription	Adipose Nuclei	Adipose
46	chr12:59301400-59306400	Weak transcription	Hela-S3	cervix
47	chr12:59301600-59303000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:59301600-59305000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:59301600-59306200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:59301600-59306400	Strong transcription	HUVEC	blood vessel

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