Variant report

Variant	rs59217052
Chromosome Location	chr3:158452456-158452457
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	chr3:158450862..158452910-chr3:158453728..158455529,2	K562	blood:
2	chr3:158387127..158389095-chr3:158450464..158453049,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079257	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs4264773	0.86[ASN][1000 genomes]
rs55835802	0.86[ASN][1000 genomes]
rs58152433	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59313096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59918529	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59957986	1.00[ASN][1000 genomes]
rs61080878	0.86[ASN][1000 genomes]
rs61387735	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61558956	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61696028	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441222	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67301795	0.86[ASN][1000 genomes]
rs67305172	0.86[ASN][1000 genomes]
rs67446837	0.86[ASN][1000 genomes]
rs6775607	0.86[ASN][1000 genomes]
rs6788069	1.00[ASN][1000 genomes]
rs73015629	0.80[EUR][1000 genomes]
rs73015644	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015649	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73015651	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015652	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015654	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015655	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015657	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015665	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015669	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73017536	1.00[ASN][1000 genomes]
rs73017539	1.00[ASN][1000 genomes]
rs73017540	1.00[ASN][1000 genomes]
rs73017541	1.00[ASN][1000 genomes]
rs73158333	0.86[ASN][1000 genomes]
rs73158334	0.86[ASN][1000 genomes]
rs7609656	0.87[EUR][1000 genomes]
rs7617304	0.86[ASN][1000 genomes]
rs7621322	0.93[EUR][1000 genomes]
rs7624161	1.00[ASN][1000 genomes]
rs7636023	1.00[ASN][1000 genomes]
rs7646881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646987	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864589	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450400-158460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:158450600-158453000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
5	chr3:158450800-158452600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:158450800-158452600	Weak transcription	Brain Angular Gyrus	brain
7	chr3:158450800-158452600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:158450800-158453000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:158450800-158455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:158450800-158460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
14	chr3:158451000-158452600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:158451000-158452600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:158451000-158452600	Weak transcription	NHLF	lung
17	chr3:158451000-158452800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:158451000-158452800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:158451000-158452800	Weak transcription	Ovary	ovary
20	chr3:158451000-158453200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:158451000-158455800	Weak transcription	Osteobl	bone
22	chr3:158451000-158457000	Weak transcription	Pancreas	Pancrea
23	chr3:158451000-158458800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:158451000-158459800	Weak transcription	Fetal Brain Male	brain
25	chr3:158451000-158459800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:158451000-158460000	Weak transcription	Fetal Intestine Large	intestine
27	chr3:158451000-158462000	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:158451000-158463400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:158451000-158463800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:158451000-158464000	Weak transcription	Colonic Mucosa	Colon
31	chr3:158451000-158464400	Weak transcription	NH-A	brain
32	chr3:158451000-158464800	Weak transcription	Gastric	stomach
33	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
35	chr3:158451200-158452600	Weak transcription	Adipose Nuclei	Adipose
36	chr3:158451200-158452600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:158451600-158452800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr3:158451600-158453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:158451600-158453600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:158451800-158452600	Strong transcription	Fetal Stomach	stomach
41	chr3:158451800-158452800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:158451800-158453600	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr3:158451800-158461400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
45	chr3:158452000-158453600	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr3:158452200-158452600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:158452200-158452600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:158452200-158453400	ZNF genes & repeats	Fetal Brain Female	brain
49	chr3:158452200-158455400	Strong transcription	Fetal Lung	lung
50	chr3:158452200-158456400	Weak transcription	Lung	lung

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