Variant report

Variant	rs59580282
Chromosome Location	chr3:23636674-23636675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBE2E2-1	chr3:23636612-23636741	XLOC_002597
2	lnc-UBE2E2-1	chr3:23636612-23636774	XLOC_002597
3	lnc-UBE2E2-1	chr3:23634971-23637228	NONHSAT088673

Extended variants
information (count: 57 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11914576	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926217	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12486880	0.82[EUR][1000 genomes]
rs12637722	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17013412	0.85[ASN][1000 genomes]
rs1826847	0.85[ASN][1000 genomes]
rs2133330	0.93[ASN][1000 genomes]
rs34710747	0.90[ASN][1000 genomes]
rs4642064	0.95[ASN][1000 genomes]
rs55666330	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55732421	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55779138	0.80[EUR][1000 genomes]
rs55894729	0.80[AFR][1000 genomes]
rs56132801	0.90[AFR][1000 genomes]
rs56964757	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57172051	0.88[ASN][1000 genomes]
rs57258152	0.93[ASN][1000 genomes]
rs57278918	0.94[ASN][1000 genomes]
rs57604595	0.88[ASN][1000 genomes]
rs57801020	0.90[ASN][1000 genomes]
rs57989144	0.91[AFR][1000 genomes]
rs58068931	0.93[ASN][1000 genomes]
rs58486254	0.91[ASN][1000 genomes]
rs60221455	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60759404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61363919	0.82[AFR][1000 genomes]
rs6550765	0.82[EUR][1000 genomes]
rs66900833	0.83[EUR][1000 genomes]
rs6775891	0.82[EUR][1000 genomes]
rs6775907	0.82[EUR][1000 genomes]
rs6778020	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6781388	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6782079	0.82[EUR][1000 genomes]
rs6799118	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800822	0.90[AFR][1000 genomes]
rs6802488	0.83[EUR][1000 genomes]
rs6807788	0.86[ASN][1000 genomes]
rs73043636	0.93[ASN][1000 genomes]
rs73043687	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73045615	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73045617	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73045660	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73049414	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7610906	0.85[ASN][1000 genomes]
rs7620266	0.93[ASN][1000 genomes]
rs7628135	0.83[EUR][1000 genomes]
rs7628949	0.83[EUR][1000 genomes]
rs7631705	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632814	0.93[ASN][1000 genomes]
rs7640458	0.90[ASN][1000 genomes]
rs7643270	0.93[ASN][1000 genomes]
rs9812300	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv460479	chr3:23626919-23807550	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv589949	chr3:23626919-23807550	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23606000-23643000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:23607000-23640400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:23609400-23637800	Weak transcription	HSMMtube	muscle
4	chr3:23621000-23642800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:23622400-23637800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:23624400-23641600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:23625400-23637800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:23628800-23647200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:23629600-23637600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr3:23629800-23637800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:23629800-23640800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:23630000-23637800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:23630000-23637800	Weak transcription	Aorta	Aorta
14	chr3:23630600-23641000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:23631400-23637800	Weak transcription	Esophagus	oesophagus
16	chr3:23631400-23643200	Weak transcription	Left Ventricle	heart
17	chr3:23631600-23637800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:23631600-23637800	Weak transcription	HSMM	muscle
19	chr3:23631800-23637800	Weak transcription	Liver	Liver
20	chr3:23632200-23637800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:23632600-23640600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:23632600-23642400	Weak transcription	Brain Angular Gyrus	brain
23	chr3:23632800-23637800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:23632800-23637800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:23632800-23637800	Weak transcription	Adipose Nuclei	Adipose
26	chr3:23632800-23637800	Weak transcription	Ovary	ovary
27	chr3:23632800-23638000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:23632800-23643200	Weak transcription	Right Ventricle	heart
29	chr3:23632800-23647200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:23633200-23638000	Weak transcription	Fetal Lung	lung
31	chr3:23633400-23637600	Weak transcription	Fetal Heart	heart
32	chr3:23633400-23637800	Weak transcription	Fetal Stomach	stomach
33	chr3:23634600-23641600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:23635000-23640600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:23635400-23642000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr3:23635600-23637800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:23635600-23638800	Strong transcription	Primary B cells from cord blood	blood
38	chr3:23635800-23641400	Weak transcription	Psoas Muscle	Psoas
39	chr3:23636200-23636800	Genic enhancers	NHLF	lung
40	chr3:23636400-23636800	Enhancers	HUVEC	blood vessel
41	chr3:23636400-23637800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:23636400-23637800	Weak transcription	Fetal Thymus	thymus
43	chr3:23636600-23636800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:23636600-23637000	Enhancers	A549	lung
45	chr3:23636600-23637000	Enhancers	NHDF-Ad	bronchial
46	chr3:23636600-23637200	Enhancers	Fetal Kidney	kidney
47	chr3:23636600-23637600	Weak transcription	GM12878-XiMat	blood
48	chr3:23636600-23641400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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