Variant report

Variant	rs55997050
Chromosome Location	chr3:160528145-160528146
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	chr3:160521593..160523754-chr3:160526329..160528531,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1455870	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1455871	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831442	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16831457	0.94[EUR][1000 genomes]
rs16831471	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16831473	1.00[EUR][1000 genomes]
rs16831516	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831520	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236620	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17236641	0.91[EUR][1000 genomes]
rs17236648	1.00[EUR][1000 genomes]
rs17236655	1.00[EUR][1000 genomes]
rs17236662	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826352	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17826358	0.94[EUR][1000 genomes]
rs17826364	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826370	1.00[EUR][1000 genomes]
rs17826376	1.00[EUR][1000 genomes]
rs2068817	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34035435	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3907061	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549318	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627794	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55891037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55905728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923270	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083575	1.00[EUR][1000 genomes]
rs56141155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157815	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180903	1.00[EUR][1000 genomes]
rs56331465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57828617	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891820	1.00[EUR][1000 genomes]
rs6771910	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779461	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73877952	1.00[EUR][1000 genomes]
rs73877966	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618082	1.00[EUR][1000 genomes]
rs7618596	1.00[EUR][1000 genomes]
rs7629154	1.00[EUR][1000 genomes]
rs7633401	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160520400-160529600	Weak transcription	Colonic Mucosa	Colon
2	chr3:160522800-160529000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:160523000-160532800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:160523200-160528600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:160525800-160528800	Enhancers	Liver	Liver
6	chr3:160525800-160529000	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:160525800-160529000	Enhancers	Brain Hippocampus Middle	brain
8	chr3:160525800-160530200	Enhancers	Adipose Nuclei	Adipose
9	chr3:160525800-160530400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:160525800-160530600	Enhancers	Fetal Brain Female	brain
11	chr3:160525800-160530800	Enhancers	Fetal Brain Male	brain
12	chr3:160526000-160528200	Enhancers	Right Atrium	heart
13	chr3:160526000-160528400	Enhancers	Aorta	Aorta
14	chr3:160526000-160528400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr3:160526000-160528400	Enhancers	Left Ventricle	heart
16	chr3:160526000-160528600	Enhancers	Brain Substantia Nigra	brain
17	chr3:160526000-160528800	Enhancers	Brain Angular Gyrus	brain
18	chr3:160526000-160528800	Enhancers	Fetal Muscle Leg	muscle
19	chr3:160526000-160529200	Enhancers	Rectal Smooth Muscle	rectum
20	chr3:160526000-160530200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:160526000-160530600	Enhancers	Colon Smooth Muscle	Colon
22	chr3:160526200-160528200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:160526200-160528600	Enhancers	Ovary	ovary
24	chr3:160526400-160530600	Enhancers	Brain Anterior Caudate	brain
25	chr3:160526600-160528400	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr3:160526600-160529000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:160526600-160529800	Enhancers	NHDF-Ad	bronchial
28	chr3:160526600-160530400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:160526600-160530400	Weak transcription	Fetal Heart	heart
30	chr3:160526800-160529800	Weak transcription	Gastric	stomach
31	chr3:160527200-160528600	Enhancers	Right Ventricle	heart
32	chr3:160527200-160528600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr3:160527400-160528400	Weak transcription	Brain Germinal Matrix	brain
34	chr3:160527400-160528600	Enhancers	HSMMtube	muscle
35	chr3:160527400-160529200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:160527400-160530600	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:160527600-160528200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:160527600-160529600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr3:160527600-160529600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:160527800-160528200	Enhancers	Osteobl	bone
41	chr3:160527800-160528400	Weak transcription	Pancreas	Pancrea
42	chr3:160527800-160530600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:160528000-160528200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr3:160528000-160528200	Enhancers	Hela-S3	cervix
45	chr3:160528000-160528800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:160528000-160529600	Weak transcription	Psoas Muscle	Psoas

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