Variant report

Variant	rs73877966
Chromosome Location	chr3:160525060-160525061
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	chr3:160473409..160475816-chr3:160524356..160526405,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1455870	0.94[EUR][1000 genomes]
rs1455871	0.94[EUR][1000 genomes]
rs16831442	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16831457	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831473	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831475	0.82[AFR][1000 genomes]
rs16831478	0.82[AFR][1000 genomes]
rs16831516	0.94[EUR][1000 genomes]
rs16831520	0.94[EUR][1000 genomes]
rs17236620	0.94[EUR][1000 genomes]
rs17236641	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17236648	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236655	1.00[EUR][1000 genomes]
rs17236662	0.94[EUR][1000 genomes]
rs17826352	0.94[EUR][1000 genomes]
rs17826358	0.94[EUR][1000 genomes]
rs17826364	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17826370	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17826376	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068817	0.94[EUR][1000 genomes]
rs34035435	0.97[EUR][1000 genomes]
rs3907061	0.94[EUR][1000 genomes]
rs4549318	0.97[EUR][1000 genomes]
rs4627794	1.00[EUR][1000 genomes]
rs55891037	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55905728	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55923270	0.94[EUR][1000 genomes]
rs55997050	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56083575	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56141155	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56157815	1.00[EUR][1000 genomes]
rs56180903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56331465	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57828617	0.94[EUR][1000 genomes]
rs58891820	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771910	0.94[EUR][1000 genomes]
rs6779461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73877952	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73877964	0.80[AFR][1000 genomes]
rs7618082	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618596	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629154	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633282	0.82[AFR][1000 genomes]
rs7633401	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160515400-160526400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:160520200-160525800	Weak transcription	Liver	Liver
3	chr3:160520200-160526000	Weak transcription	Aorta	Aorta
4	chr3:160520200-160526000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:160520200-160526400	Weak transcription	Stomach Mucosa	stomach
6	chr3:160520400-160526400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:160520400-160529600	Weak transcription	Colonic Mucosa	Colon
8	chr3:160521000-160526000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:160521000-160526000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:160521000-160526000	Weak transcription	Right Atrium	heart
11	chr3:160521000-160526000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:160521000-160526400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:160522000-160525200	Enhancers	Colon Smooth Muscle	Colon
14	chr3:160522800-160525200	Weak transcription	Brain Germinal Matrix	brain
15	chr3:160522800-160525800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:160522800-160526000	Weak transcription	Gastric	stomach
17	chr3:160522800-160527600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:160522800-160529000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:160523000-160525800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:160523000-160526000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:160523000-160526000	Weak transcription	Brain Substantia Nigra	brain
22	chr3:160523000-160526000	Weak transcription	Pancreas	Pancrea
23	chr3:160523000-160526200	Weak transcription	Esophagus	oesophagus
24	chr3:160523000-160526200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:160523000-160526400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:160523000-160532800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:160523200-160526000	Weak transcription	Fetal Heart	heart
28	chr3:160523200-160526400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:160523200-160528600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:160523400-160526200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:160523400-160527400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:160523800-160526000	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:160524000-160525800	Weak transcription	Fetal Brain Male	brain
34	chr3:160524200-160525400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:160524200-160526000	Weak transcription	Left Ventricle	heart
36	chr3:160524200-160527200	Weak transcription	Right Ventricle	heart
37	chr3:160524400-160525800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:160524400-160525800	Weak transcription	Adipose Nuclei	Adipose
39	chr3:160524400-160525800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:160524400-160526000	Weak transcription	Psoas Muscle	Psoas
41	chr3:160524400-160526000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:160524600-160525200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:160524800-160525800	Weak transcription	Fetal Brain Female	brain
44	chr3:160525000-160526400	Enhancers	Skeletal Muscle Female	skeletal muscle

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