Variant report

Variant	rs58528592
Chromosome Location	chr3:52755379-52755380
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52739833..52741982-chr3:52754978..52756987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114902	Chromatin interaction
ENSG00000016864	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11510435	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[EUR][1000 genomes]
rs17052357	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052404	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.93[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56665533	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58564212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59869286	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	0.83[AFR][1000 genomes]
rs72950424	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	0.86[AFR][1000 genomes];1.00[EUR][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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741400-52765600	Weak transcription	Aorta	Aorta
2	chr3:52741400-52766600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:52741600-52764000	Weak transcription	Small Intestine	intestine
4	chr3:52741600-52765600	Weak transcription	Esophagus	oesophagus
5	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
6	chr3:52742000-52765600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:52742000-52766400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:52742000-52766400	Weak transcription	NHLF	lung
9	chr3:52742000-52766600	Weak transcription	Hela-S3	cervix
10	chr3:52742000-52766600	Weak transcription	NHEK	skin
11	chr3:52742200-52767200	Weak transcription	Fetal Brain Male	brain
12	chr3:52742200-52768800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:52742400-52764200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:52742400-52771400	Weak transcription	K562	blood
15	chr3:52742400-52772800	Weak transcription	Pancreas	Pancrea
16	chr3:52742600-52766000	Weak transcription	HUVEC	blood vessel
17	chr3:52743000-52766600	Weak transcription	NH-A	brain
18	chr3:52743000-52766600	Weak transcription	NHDF-Ad	bronchial
19	chr3:52743200-52766600	Weak transcription	Osteobl	bone
20	chr3:52743600-52755400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:52743600-52764200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:52744000-52764200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:52744000-52764200	Weak transcription	Fetal Kidney	kidney
24	chr3:52744000-52765400	Weak transcription	HMEC	breast
25	chr3:52744600-52764200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:52744800-52767000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:52746800-52764400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:52747000-52763800	Weak transcription	Left Ventricle	heart
29	chr3:52747000-52765400	Weak transcription	Spleen	Spleen
30	chr3:52747000-52765600	Weak transcription	Brain Anterior Caudate	brain
31	chr3:52747000-52766600	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:52749000-52756600	Weak transcription	Lung	lung
33	chr3:52749000-52764800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:52749000-52771600	Weak transcription	Colonic Mucosa	Colon
35	chr3:52749200-52756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:52749200-52761400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:52749200-52762000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:52749200-52764400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:52749200-52766800	Weak transcription	Right Ventricle	heart
40	chr3:52749200-52767000	Weak transcription	Fetal Heart	heart
41	chr3:52749200-52767400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:52749200-52779800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:52749400-52758200	Weak transcription	Stomach Mucosa	stomach
44	chr3:52749400-52760800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:52749400-52763800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:52749400-52764200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:52749400-52764200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:52749400-52764200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:52749400-52766600	Weak transcription	Gastric	stomach
50	chr3:52749400-52776200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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