Variant report

Variant	rs55954252
Chromosome Location	chr3:111584990-111584991
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	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	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17425250	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17490701	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17491175	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55921603	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56092121	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56105878	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343172	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67396907	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809779	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73226343	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73226349	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73226359	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73226368	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73226399	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73228506	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73228508	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228510	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228514	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228515	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228518	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228521	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228530	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228535	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73228543	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73228545	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228547	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228550	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73228569	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7340610	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs937557	0.95[AMR][1000 genomes];0.95[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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111579400-111585000	Weak transcription	Gastric	stomach
2	chr3:111579800-111588400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:111579800-111589000	Weak transcription	Pancreas	Pancrea
4	chr3:111580000-111589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:111580600-111585800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:111580800-111585200	Enhancers	HMEC	breast
7	chr3:111581400-111586000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr3:111581400-111593800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:111581800-111585600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:111582200-111585000	Weak transcription	Left Ventricle	heart
11	chr3:111582200-111585000	Weak transcription	Spleen	Spleen
12	chr3:111582200-111585400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:111582200-111585800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:111582200-111586800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:111582200-111586800	Weak transcription	Placenta	Placenta
16	chr3:111582200-111593200	Weak transcription	Lung	lung
17	chr3:111583000-111587600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:111583200-111585200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:111583200-111585200	Enhancers	Fetal Muscle Leg	muscle
20	chr3:111583600-111585200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:111583600-111585600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:111583600-111586000	Enhancers	Right Atrium	heart
23	chr3:111583800-111591200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:111584000-111585400	Enhancers	Ovary	ovary
25	chr3:111584000-111585600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:111584000-111586000	Enhancers	NH-A	brain
27	chr3:111584000-111587200	Enhancers	Right Ventricle	heart
28	chr3:111584200-111585200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:111584200-111585400	Enhancers	Psoas Muscle	Psoas
30	chr3:111584200-111585400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:111584400-111585000	Enhancers	Adipose Nuclei	Adipose
32	chr3:111584400-111585000	Weak transcription	Aorta	Aorta
33	chr3:111584400-111585000	Enhancers	Stomach Smooth Muscle	stomach
34	chr3:111584400-111585000	Enhancers	Osteobl	bone
35	chr3:111584400-111585200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:111584400-111585200	Weak transcription	Small Intestine	intestine
37	chr3:111584400-111585200	Enhancers	NHLF	lung
38	chr3:111584400-111585400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr3:111584400-111585400	Enhancers	HSMM	muscle
40	chr3:111584400-111587000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:111584400-111587200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:111584400-111587600	Weak transcription	NHEK	skin
43	chr3:111584400-111587800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:111584400-111589200	Enhancers	Colon Smooth Muscle	Colon
45	chr3:111584400-111589800	Enhancers	Rectal Smooth Muscle	rectum
46	chr3:111584400-111591000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:111584600-111585000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:111584600-111585000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:111584600-111585000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:111584600-111585200	Enhancers	HSMMtube	muscle

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