Variant report

Variant	rs9725163
Chromosome Location	chr1:180883724-180883725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180882477..180885786-chr1:180922759..180925050,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232586	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12089469	1.00[AMR][1000 genomes]
rs17301581	1.00[AMR][1000 genomes]
rs17301602	1.00[AMR][1000 genomes]
rs17301762	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17301936	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17302040	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17302075	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17302102	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17373501	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17373660	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17374151	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3845409	0.83[AMR][1000 genomes]
rs3908047	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55960112	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59077359	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809342	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809345	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809347	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809350	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809351	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809352	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61809353	0.80[AMR][1000 genomes]
rs61809354	1.00[AMR][1000 genomes]
rs61809355	1.00[AMR][1000 genomes]
rs61809356	1.00[AMR][1000 genomes]
rs61809357	1.00[AMR][1000 genomes]
rs61809358	1.00[AMR][1000 genomes]
rs61811160	1.00[AMR][1000 genomes]
rs61811190	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811191	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811192	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811193	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811197	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811199	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811202	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811204	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811221	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811222	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811223	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61811224	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61811225	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61811227	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61811245	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61811248	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6664966	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6674012	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6697299	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72707419	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72707494	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72723006	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72723010	1.00[AMR][1000 genomes]
rs72723014	1.00[AMR][1000 genomes]
rs72723023	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72723026	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72723027	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72723035	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72723043	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180882400-180894600	Weak transcription	Pancreas	Pancrea
2	chr1:180882600-180894000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:180882800-180884400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:180882800-180885000	Weak transcription	Ovary	ovary
5	chr1:180882800-180885800	Weak transcription	Lung	lung
6	chr1:180882800-180886000	Weak transcription	Brain Anterior Caudate	brain
7	chr1:180882800-180886200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:180882800-180887000	Weak transcription	Spleen	Spleen
9	chr1:180882800-180887200	Weak transcription	Placenta	Placenta
10	chr1:180882800-180887400	Weak transcription	Gastric	stomach
11	chr1:180882800-180888000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:180882800-180889400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:180882800-180891200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:180882800-180892600	Weak transcription	Esophagus	oesophagus
15	chr1:180882800-180894400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:180883000-180885600	Weak transcription	Aorta	Aorta
17	chr1:180883000-180885600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:180883000-180885800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:180883000-180886800	Weak transcription	HSMMtube	muscle
20	chr1:180883000-180891200	Weak transcription	Fetal Brain Female	brain
21	chr1:180883000-180891600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:180883000-180892200	Weak transcription	Brain Germinal Matrix	brain
23	chr1:180883000-180894600	Weak transcription	Right Ventricle	heart
24	chr1:180883000-180894800	Weak transcription	Colonic Mucosa	Colon
25	chr1:180883200-180884200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:180883200-180885000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:180883200-180885600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:180883200-180892200	Weak transcription	Right Atrium	heart
29	chr1:180883200-180894200	Weak transcription	Brain Angular Gyrus	brain
30	chr1:180883400-180887800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:180883400-180892600	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:180883600-180883800	Enhancers	Fetal Muscle Leg	muscle
33	chr1:180883600-180883800	Enhancers	Fetal Stomach	stomach
34	chr1:180883600-180884400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:180883600-180884600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:180883600-180885200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:180883600-180885200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:180883600-180885400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:180883600-180885400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:180883600-180885400	Weak transcription	NHLF	lung
41	chr1:180883600-180885400	Weak transcription	Osteobl	bone
42	chr1:180883600-180885600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:180883600-180885600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:180883600-180885600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:180883600-180886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:180883600-180886000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:180883600-180886200	Weak transcription	NHDF-Ad	bronchial
48	chr1:180883600-180886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:180883600-180886800	Weak transcription	Left Ventricle	heart
50	chr1:180883600-180887200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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