Variant report

Variant	rs28454853
Chromosome Location	chr12:117494142-117494143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117491735..117493478-chr12:117493930..117496851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088992	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10850749	1.00[ASN][1000 genomes]
rs11068233	1.00[EUR][1000 genomes]
rs11068265	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068267	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068268	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068275	0.96[ASN][1000 genomes]
rs11068278	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068279	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068285	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068288	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068304	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068305	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227740	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228058	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230860	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12297748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301340	1.00[AMR][1000 genomes]
rs12305518	1.00[AMR][1000 genomes]
rs12313807	1.00[ASN][1000 genomes]
rs12313968	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318749	1.00[ASN][1000 genomes]
rs17582998	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17583110	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57066310	1.00[ASN][1000 genomes]
rs57212223	1.00[ASN][1000 genomes]
rs58547422	1.00[ASN][1000 genomes]
rs59143111	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60601556	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72487544	1.00[EUR][1000 genomes];0.96[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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117483800-117498000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:117483800-117498200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:117483800-117498200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:117484400-117497800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:117484800-117498200	Weak transcription	Thymus	Thymus
6	chr12:117486600-117500400	Weak transcription	Fetal Lung	lung
7	chr12:117486800-117498800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:117487200-117500400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:117487400-117494200	Weak transcription	A549	lung
10	chr12:117487400-117497000	Weak transcription	Ovary	ovary
11	chr12:117488600-117496800	Weak transcription	Right Atrium	heart
12	chr12:117489600-117500400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:117490800-117498200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:117491000-117496200	Strong transcription	Dnd41	blood
15	chr12:117491000-117498400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:117491200-117496200	Strong transcription	HepG2	liver
17	chr12:117491200-117498000	Weak transcription	K562	blood
18	chr12:117491400-117496600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:117491400-117498400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:117491400-117498600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:117491600-117495200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:117491600-117496400	Weak transcription	Stomach Mucosa	stomach
23	chr12:117491600-117496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:117491600-117498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:117491600-117498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:117491600-117500400	Weak transcription	GM12878-XiMat	blood
27	chr12:117491800-117494400	Weak transcription	Left Ventricle	heart
28	chr12:117491800-117494800	Strong transcription	Fetal Stomach	stomach
29	chr12:117491800-117496400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:117491800-117496400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:117491800-117496800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:117491800-117496800	Weak transcription	Brain Anterior Caudate	brain
33	chr12:117492200-117496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:117492200-117496800	Weak transcription	Right Ventricle	heart
35	chr12:117492600-117495400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:117492600-117496800	Weak transcription	Spleen	Spleen
37	chr12:117492800-117495000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:117493000-117494800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr12:117493000-117498400	Weak transcription	Placenta	Placenta
40	chr12:117493200-117494600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:117493200-117497800	Weak transcription	Primary B cells from cord blood	blood
42	chr12:117493400-117496600	Weak transcription	Gastric	stomach
43	chr12:117493600-117495200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:117493600-117496000	Weak transcription	Fetal Heart	heart
45	chr12:117493600-117496600	Weak transcription	Pancreas	Pancrea

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