Variant report

Variant	rs58558806
Chromosome Location	chr3:53291134-53291135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53268810..53273941-chr3:53286770..53291307,7	MCF-7	breast:
2	chr3:53268931..53277907-chr3:53285563..53291617,11	MCF-7	breast:
3	chr3:53288526..53291244-chr3:53879304..53881119,2	MCF-7	breast:
4	chr3:53187844..53191099-chr3:53288490..53291420,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000056736	Chromatin interaction
ENSG00000163931	Chromatin interaction
ENSG00000163932	Chromatin interaction
ENSG00000016391	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10433617	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433618	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108506	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17234771	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235667	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41275543	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56654807	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59145995	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255993	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255994	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255999	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256000	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256003	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256009	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256043	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256049	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256050	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62256053	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256965	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256966	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256968	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256969	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62257004	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257007	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257009	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257011	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257013	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257024	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6780100	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73080266	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73082274	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7622159	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830594	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830895	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846315	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9850440	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864057	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53289400-53293400	Weak transcription	Fetal Heart	heart
2	chr3:53290000-53291200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:53290000-53291400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:53290000-53292600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:53290000-53295800	Weak transcription	Gastric	stomach
6	chr3:53290200-53293400	Weak transcription	Lung	lung
7	chr3:53290400-53291200	Enhancers	HepG2	liver
8	chr3:53290400-53291600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:53290400-53291600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:53290400-53291800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:53290400-53292200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:53290400-53292200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:53290400-53292200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:53290400-53292400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:53290400-53292400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:53290400-53292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:53290400-53292400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:53290400-53292400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:53290400-53292400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:53290400-53292400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:53290400-53292400	Weak transcription	Hela-S3	cervix
22	chr3:53290400-53292600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:53290400-53292600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:53290400-53292600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:53290400-53292600	Weak transcription	Brain Substantia Nigra	brain
26	chr3:53290400-53292800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:53290400-53292800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:53290400-53293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:53290400-53293000	Weak transcription	Fetal Lung	lung
30	chr3:53290400-53293000	Weak transcription	HSMMtube	muscle
31	chr3:53290400-53293200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:53290400-53293200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:53290400-53293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:53290400-53293200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:53290400-53293200	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:53290400-53293200	Weak transcription	Left Ventricle	heart
37	chr3:53290400-53293200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:53290400-53293200	Weak transcription	NHDF-Ad	bronchial
39	chr3:53290400-53293400	Weak transcription	Ovary	ovary
40	chr3:53290400-53293400	Weak transcription	Right Atrium	heart
41	chr3:53290400-53293400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:53290400-53293400	Weak transcription	HSMM	muscle
43	chr3:53290400-53293400	Enhancers	K562	blood
44	chr3:53290400-53293400	Weak transcription	NHLF	lung
45	chr3:53290400-53294000	Weak transcription	Psoas Muscle	Psoas
46	chr3:53290400-53294200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:53290400-53294800	Weak transcription	NHEK	skin
48	chr3:53290400-53295000	Enhancers	A549	lung
49	chr3:53290400-53295800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:53290400-53295800	Weak transcription	Spleen	Spleen

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