Variant report

Variant	rs58562675
Chromosome Location	chr15:42790982-42790983
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42781216..42785618-chr15:42786050..42793334,15	K562	blood:
2	chr15:42786351..42790033-chr15:42790160..42794805,5	K562	blood:
3	chr15:42782381..42786334-chr15:42789829..42792638,5	K562	blood:

Variant related genes	Relation type
ENSG00000092531	Chromatin interaction
ENSG00000103994	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1044866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11541527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973349	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090286	0.84[AFR][1000 genomes]
rs5009460	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57249373	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57349778	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58122107	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58952814	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59058205	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59091063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60060355	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60168929	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60606292	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60697170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60839827	1.00[AMR][1000 genomes]
rs61368952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61474811	0.85[AMR][1000 genomes]
rs6493048	0.95[AFR][1000 genomes]
rs6493049	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493050	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166143	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166633	0.87[AMR][1000 genomes]
rs7172064	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7172955	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7175059	0.87[AMR][1000 genomes]
rs7178822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7181938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402762	0.85[AMR][1000 genomes]
rs73402776	0.85[AMR][1000 genomes]
rs73402796	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404708	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404711	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404725	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404729	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404754	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404758	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404768	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404774	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404775	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406503	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406505	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406509	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406526	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406531	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406544	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406553	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406557	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs768118	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8023948	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8027207	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031383	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033555	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033810	1.00[AMR][1000 genomes]
rs8034001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8035877	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8036927	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8037277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040624	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42788400-42808000	Weak transcription	Esophagus	oesophagus
2	chr15:42788600-42791000	Enhancers	Primary B cells from peripheral blood	blood
3	chr15:42788600-42791400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:42788600-42792400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr15:42788600-42798400	Weak transcription	Ovary	ovary
6	chr15:42788600-42805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:42788600-42806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:42788600-42807200	Weak transcription	Fetal Kidney	kidney
9	chr15:42788800-42791400	Weak transcription	NH-A	brain
10	chr15:42788800-42792000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:42788800-42792200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:42788800-42792200	Weak transcription	Right Atrium	heart
13	chr15:42788800-42792400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:42788800-42793000	Weak transcription	Brain Substantia Nigra	brain
15	chr15:42788800-42793600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:42788800-42797000	Weak transcription	HSMMtube	muscle
17	chr15:42788800-42800400	Weak transcription	Fetal Lung	lung
18	chr15:42788800-42805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:42788800-42805400	Weak transcription	Brain Germinal Matrix	brain
20	chr15:42789000-42791000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:42789000-42791000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr15:42789000-42791200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:42789000-42791600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:42789000-42791600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:42789000-42791800	Enhancers	Duodenum Mucosa	Duodenum
26	chr15:42789000-42791800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:42789000-42792000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:42789000-42792000	Weak transcription	NHLF	lung
29	chr15:42789000-42792200	Weak transcription	Fetal Heart	heart
30	chr15:42789000-42792400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:42789000-42793000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr15:42789000-42794000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:42789000-42797000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:42789000-42797000	Weak transcription	Brain Angular Gyrus	brain
35	chr15:42789000-42803400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:42789000-42805400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:42789000-42806400	Weak transcription	Thymus	Thymus
38	chr15:42789200-42791000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:42789200-42791000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:42789200-42791000	Weak transcription	HSMM	muscle
41	chr15:42789200-42791000	Enhancers	HUVEC	blood vessel
42	chr15:42789200-42791200	Weak transcription	Colonic Mucosa	Colon
43	chr15:42789200-42791800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:42789200-42791800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:42789200-42792000	Weak transcription	Fetal Muscle Leg	muscle
46	chr15:42789200-42792600	Enhancers	Fetal Intestine Large	intestine
47	chr15:42789200-42793000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr15:42789200-42793000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:42789200-42793200	Weak transcription	Brain Anterior Caudate	brain
50	chr15:42789200-42794000	Enhancers	Placenta	Placenta

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