Variant report

Variant	rs3908047
Chromosome Location	chr1:180884799-180884800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180880902..180883587-chr1:180884208..180886874,3	MCF-7	breast:
2	chr1:180882477..180885786-chr1:180922759..180925050,3	MCF-7	breast:
3	chr1:180884197..180885718-chr4:69153705..69156603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135835	Chromatin interaction
ENSG00000232586	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs12089469	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17301581	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17301602	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17301762	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17301936	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17302040	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17302075	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17302102	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17373501	0.88[EUR][1000 genomes]
rs17373660	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17374151	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55960112	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59077359	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61809342	0.88[EUR][1000 genomes]
rs61809345	0.88[EUR][1000 genomes]
rs61809347	0.88[EUR][1000 genomes]
rs61809350	0.88[EUR][1000 genomes]
rs61809351	0.88[EUR][1000 genomes]
rs61809352	0.88[EUR][1000 genomes]
rs61809353	0.84[EUR][1000 genomes]
rs61809354	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61809355	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61809356	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61809357	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61809358	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61811160	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61811190	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811191	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811192	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811193	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811197	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811199	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811202	0.88[EUR][1000 genomes]
rs61811204	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811221	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811222	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61811223	0.92[EUR][1000 genomes]
rs61811224	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811225	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811227	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61811245	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811248	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6664966	0.88[EUR][1000 genomes]
rs6674012	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6697299	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72707419	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72707494	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72723006	0.88[EUR][1000 genomes]
rs72723010	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72723014	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72723023	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72723026	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72723027	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72723035	0.88[EUR][1000 genomes]
rs72723043	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9725163	0.91[AMR][1000 genomes];0.94[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:60 , 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	chr1:180882800-180885000	Weak transcription	Ovary	ovary
4	chr1:180882800-180885800	Weak transcription	Lung	lung
5	chr1:180882800-180886000	Weak transcription	Brain Anterior Caudate	brain
6	chr1:180882800-180886200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:180882800-180887000	Weak transcription	Spleen	Spleen
8	chr1:180882800-180887200	Weak transcription	Placenta	Placenta
9	chr1:180882800-180887400	Weak transcription	Gastric	stomach
10	chr1:180882800-180888000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:180882800-180889400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:180882800-180891200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:180882800-180892600	Weak transcription	Esophagus	oesophagus
14	chr1:180882800-180894400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:180883000-180885600	Weak transcription	Aorta	Aorta
16	chr1:180883000-180885600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:180883000-180885800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:180883000-180886800	Weak transcription	HSMMtube	muscle
19	chr1:180883000-180891200	Weak transcription	Fetal Brain Female	brain
20	chr1:180883000-180891600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:180883000-180892200	Weak transcription	Brain Germinal Matrix	brain
22	chr1:180883000-180894600	Weak transcription	Right Ventricle	heart
23	chr1:180883000-180894800	Weak transcription	Colonic Mucosa	Colon
24	chr1:180883200-180885000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:180883200-180885600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:180883200-180892200	Weak transcription	Right Atrium	heart
27	chr1:180883200-180894200	Weak transcription	Brain Angular Gyrus	brain
28	chr1:180883400-180887800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:180883400-180892600	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:180883600-180885200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:180883600-180885200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:180883600-180885400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:180883600-180885400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:180883600-180885400	Weak transcription	NHLF	lung
35	chr1:180883600-180885400	Weak transcription	Osteobl	bone
36	chr1:180883600-180885600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:180883600-180885600	Weak transcription	Adipose Nuclei	Adipose
38	chr1:180883600-180885600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:180883600-180886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:180883600-180886000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:180883600-180886200	Weak transcription	NHDF-Ad	bronchial
42	chr1:180883600-180886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:180883600-180886800	Weak transcription	Left Ventricle	heart
44	chr1:180883600-180887200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:180883600-180887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:180883600-180888600	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:180883600-180891800	Weak transcription	HSMM	muscle
48	chr1:180883600-180892000	Weak transcription	Fetal Heart	heart
49	chr1:180883600-180892200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:180883600-180894200	Weak transcription	Brain Inferior Temporal Lobe	brain

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