Variant report

Variant	rs56105878
Chromosome Location	chr3:111585322-111585323
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	chr3:111583879..111585669-chr3:111695722..111698206,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144827	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17424938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17425250	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17490701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17491175	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55921603	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55954252	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56092121	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56343172	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67396907	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809779	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73226343	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73226349	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73226359	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73226368	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73226399	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73228506	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73228508	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228515	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228521	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228535	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73228543	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73228545	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228547	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228550	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228569	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7340610	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs937557	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][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	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111579800-111588400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:111579800-111589000	Weak transcription	Pancreas	Pancrea
3	chr3:111580000-111589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:111580600-111585800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:111581400-111586000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr3:111581400-111593800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:111581800-111585600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:111582200-111585400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:111582200-111585800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:111582200-111586800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:111582200-111586800	Weak transcription	Placenta	Placenta
12	chr3:111582200-111593200	Weak transcription	Lung	lung
13	chr3:111583000-111587600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:111583600-111585600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:111583600-111586000	Enhancers	Right Atrium	heart
16	chr3:111583800-111591200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:111584000-111585400	Enhancers	Ovary	ovary
18	chr3:111584000-111585600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:111584000-111586000	Enhancers	NH-A	brain
20	chr3:111584000-111587200	Enhancers	Right Ventricle	heart
21	chr3:111584200-111585400	Enhancers	Psoas Muscle	Psoas
22	chr3:111584200-111585400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:111584400-111585400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr3:111584400-111585400	Enhancers	HSMM	muscle
25	chr3:111584400-111587000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:111584400-111587200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:111584400-111587600	Weak transcription	NHEK	skin
28	chr3:111584400-111587800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:111584400-111589200	Enhancers	Colon Smooth Muscle	Colon
30	chr3:111584400-111589800	Enhancers	Rectal Smooth Muscle	rectum
31	chr3:111584400-111591000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:111584600-111585400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:111584600-111585400	Enhancers	HUVEC	blood vessel
34	chr3:111584600-111585600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:111584600-111585600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr3:111584600-111585600	Enhancers	Hela-S3	cervix
37	chr3:111584600-111586800	Weak transcription	A549	lung
38	chr3:111584600-111587200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:111584600-111587600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:111584600-111587800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:111584600-111588000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:111584600-111588400	Weak transcription	Fetal Stomach	stomach
43	chr3:111584600-111588400	Weak transcription	HepG2	liver
44	chr3:111584600-111588400	Weak transcription	NHDF-Ad	bronchial
45	chr3:111584600-111588600	Weak transcription	Fetal Lung	lung
46	chr3:111584600-111588800	Weak transcription	Stomach Mucosa	stomach
47	chr3:111584600-111590800	Weak transcription	Fetal Kidney	kidney
48	chr3:111584600-111591000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:111584600-111593200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine

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