Variant report

Variant	rs59257245
Chromosome Location	chr3:119054576-119054577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119040478..119045025-chr3:119052618..119056629,7	MCF-7	breast:
2	chr3:119041827..119043883-chr3:119053640..119055675,2	MCF-7	breast:
3	chr3:119045537..119049626-chr3:119052248..119055183,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction
ENSG00000031081	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10511389	0.86[ASN][1000 genomes]
rs12637189	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16829702	0.84[EUR][1000 genomes]
rs16829716	0.92[ASN][1000 genomes]
rs17281577	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56176656	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58374436	0.91[ASN][1000 genomes]
rs72962562	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854494	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860092	0.86[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119042600-119055600	Weak transcription	Fetal Brain Male	brain
2	chr3:119042800-119056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119042800-119070600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:119042800-119072000	Weak transcription	Thymus	Thymus
5	chr3:119043000-119069000	Weak transcription	Primary T cells from cord blood	blood
6	chr3:119043200-119062400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:119046000-119056000	Weak transcription	Fetal Thymus	thymus
8	chr3:119046000-119064200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:119046000-119064600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:119046800-119056000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:119048000-119054600	Enhancers	Fetal Heart	heart
12	chr3:119048800-119062800	Weak transcription	Osteobl	bone
13	chr3:119049200-119062200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:119049200-119071200	Weak transcription	Aorta	Aorta
15	chr3:119049400-119056000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:119049600-119068000	Weak transcription	NH-A	brain
17	chr3:119050000-119062000	Weak transcription	Placenta	Placenta
18	chr3:119050800-119056000	Weak transcription	HSMM	muscle
19	chr3:119050800-119064600	Weak transcription	HSMMtube	muscle
20	chr3:119050800-119075800	Weak transcription	Pancreas	Pancrea
21	chr3:119051000-119055400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:119051000-119064800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:119051800-119054600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:119051800-119056000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:119051800-119056200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:119052000-119055200	Weak transcription	GM12878-XiMat	blood
27	chr3:119052000-119059400	Weak transcription	HUVEC	blood vessel
28	chr3:119052000-119062000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:119052000-119064600	Weak transcription	Fetal Intestine Small	intestine
30	chr3:119052600-119054600	Enhancers	Left Ventricle	heart
31	chr3:119052600-119064200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:119053000-119054600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:119053200-119054600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:119053200-119055600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:119053200-119064800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:119053200-119087200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:119053400-119064400	Weak transcription	Psoas Muscle	Psoas
38	chr3:119053400-119064400	Weak transcription	Spleen	Spleen
39	chr3:119053400-119068200	Weak transcription	Right Ventricle	heart
40	chr3:119053400-119087000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:119053600-119055400	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:119053600-119056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:119053600-119059200	Weak transcription	Ovary	ovary
44	chr3:119053600-119064200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:119053600-119067800	Weak transcription	Fetal Lung	lung
46	chr3:119053600-119071400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:119053800-119059600	Weak transcription	Adipose Nuclei	Adipose
48	chr3:119054200-119054800	Enhancers	Right Atrium	heart
49	chr3:119054400-119054600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:119054400-119054600	Genic enhancers	Lung	lung

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