Variant report

Variant	rs28620262
Chromosome Location	chr12:58011585-58011586
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
2	chr12:58009848..58012356-chr12:58118975..58121392,2	MCF-7	breast:
3	chr12:57913091..57915646-chr12:58010883..58013272,4	K562	blood:
4	chr12:57912181..57914315-chr12:58008996..58011925,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255737	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000224713	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11172270	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578587	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7294447	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73346100	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7960103	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7966948	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7977683	0.86[ASN][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	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers 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	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58013200	Weak transcription	Gastric	stomach
2	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
3	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
4	chr12:58006800-58011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:58006800-58011600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:58006800-58011600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:58006800-58011800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:58006800-58012000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:58007000-58012000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:58008000-58012800	Weak transcription	HepG2	liver
11	chr12:58008400-58012000	Strong transcription	Aorta	Aorta
12	chr12:58009200-58011800	Strong transcription	Colon Smooth Muscle	Colon
13	chr12:58009400-58012000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:58009800-58011800	Active TSS	Left Ventricle	heart
15	chr12:58010000-58011800	Active TSS	Right Atrium	heart
16	chr12:58010200-58013600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:58010400-58011600	Weak transcription	Spleen	Spleen
18	chr12:58010400-58013600	Strong transcription	Stomach Smooth Muscle	stomach
19	chr12:58010400-58014000	Weak transcription	Brain Substantia Nigra	brain
20	chr12:58010400-58014400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:58010600-58012000	Enhancers	K562	blood
22	chr12:58010600-58012200	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:58010600-58013000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:58010600-58014000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:58010600-58014000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:58010600-58014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:58010800-58011600	Weak transcription	Brain Germinal Matrix	brain
28	chr12:58010800-58012000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:58010800-58013000	Weak transcription	Osteobl	bone
30	chr12:58010800-58013200	Weak transcription	Esophagus	oesophagus
31	chr12:58010800-58013600	Weak transcription	Brain Anterior Caudate	brain
32	chr12:58011000-58011600	Active TSS	Right Ventricle	heart
33	chr12:58011400-58011600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:58011400-58011600	Enhancers	Lung	lung
35	chr12:58011400-58011800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:58011400-58011800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:58011400-58014600	Weak transcription	Ovary	ovary

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