Variant report

Variant	rs55654954
Chromosome Location	chr12:64890476-64890477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:64890410-64890527	MCF-7	breast:	n/a	n/a
2	KAP1	chr12:64889993-64890616	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64845703..64848434-chr12:64888861..64891415,2	MCF-7	breast:
2	chr12:64886957..64889767-chr12:64890289..64894074,3	MCF-7	breast:

Variant related genes	Relation type
TBK1	TF binding region
ENSG00000183735	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11829120	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11837890	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075094	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292023	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55690537	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55999447	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56198126	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326550	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58143737	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60358746	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60520114	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61396007	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61931543	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61931544	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931545	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931549	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931550	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931552	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931555	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931557	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931558	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61933191	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933192	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933195	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933196	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933198	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933199	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933200	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933201	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933202	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933205	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61933207	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933209	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933211	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933212	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303577	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120375	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120383	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73122367	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488918	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64847000-64900800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:64853400-64896800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:64854000-64893000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:64854400-64897200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:64854600-64894000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:64854800-64893600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:64862800-64896800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:64866000-64897000	Weak transcription	Esophagus	oesophagus
9	chr12:64869600-64892000	Weak transcription	Small Intestine	intestine
10	chr12:64869600-64893000	Weak transcription	Fetal Brain Male	brain
11	chr12:64869800-64895400	Weak transcription	Fetal Kidney	kidney
12	chr12:64870000-64893600	Weak transcription	Fetal Heart	heart
13	chr12:64871000-64896000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:64871000-64908200	Weak transcription	Psoas Muscle	Psoas
15	chr12:64871200-64895000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:64871200-64897000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:64872200-64896200	Strong transcription	Liver	Liver
18	chr12:64872400-64895600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:64872400-64895800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:64872400-64896800	Strong transcription	Placenta	Placenta
21	chr12:64872600-64896000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:64873600-64895600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:64873600-64895800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:64873600-64895800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:64873800-64893600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:64874200-64896800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:64874400-64896000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:64874400-64896000	Strong transcription	Osteobl	bone
29	chr12:64875000-64895800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:64875000-64896600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:64875200-64895600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:64875400-64895400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr12:64875600-64895800	Strong transcription	Adipose Nuclei	Adipose
34	chr12:64876200-64895000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:64876800-64890800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:64878400-64895600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:64879600-64892800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:64879600-64895800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:64880600-64892000	Weak transcription	Right Ventricle	heart
40	chr12:64880600-64895200	Weak transcription	Pancreas	Pancrea
41	chr12:64881200-64892600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:64882200-64896000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:64883400-64890600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:64884000-64891200	Strong transcription	Brain Substantia Nigra	brain
45	chr12:64884200-64892200	Weak transcription	Ovary	ovary
46	chr12:64884400-64895400	Weak transcription	Brain Germinal Matrix	brain
47	chr12:64884600-64894600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:64884600-64897800	Weak transcription	Aorta	Aorta
49	chr12:64884800-64892000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:64885000-64890600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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