Variant report

Variant	rs58558817
Chromosome Location	chr8:54652396-54652397
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:54652340-54652490	WERI-Rb-1	eye:	n/a	chr8:54652426-54652439 chr8:54652423-54652441

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:54651332..54653261-chr8:54754407..54756402,2	MCF-7	breast:
2	chr8:54652211..54654707-chr8:54657866..54660858,2	MCF-7	breast:

Variant related genes	Relation type
ATP6V1H	TF binding region
ENSG00000047249	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1031979	0.92[ASN][1000 genomes]
rs1031980	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10435587	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11994467	0.88[ASN][1000 genomes]
rs11996300	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12056486	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12056719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12234972	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13276766	0.85[ASN][1000 genomes]
rs1552148	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16919507	0.83[EUR][1000 genomes]
rs16919508	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16919522	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919534	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919537	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919541	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16919563	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16919571	0.93[ASN][1000 genomes]
rs16919573	0.92[ASN][1000 genomes]
rs1872063	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1905061	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2128150	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2170444	0.92[ASN][1000 genomes]
rs2376011	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735831	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757954	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41321146	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236945	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4737192	0.90[ASN][1000 genomes]
rs4737518	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4737554	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4737558	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4737764	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4737765	0.94[ASN][1000 genomes]
rs4737821	0.93[ASN][1000 genomes]
rs4737974	0.84[EUR][1000 genomes]
rs4738027	0.84[EUR][1000 genomes]
rs4738470	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4738646	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4738701	0.90[EUR][1000 genomes]
rs4738884	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4738916	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55682919	0.90[EUR][1000 genomes]
rs55876329	0.92[ASN][1000 genomes]
rs55964335	0.90[ASN][1000 genomes]
rs56818292	0.93[ASN][1000 genomes]
rs56956173	0.84[EUR][1000 genomes]
rs56973376	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57071607	0.92[EUR][1000 genomes]
rs57550901	0.90[EUR][1000 genomes]
rs58473841	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58970885	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61070518	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6984257	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6986372	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6987427	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6988009	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6988082	0.90[EUR][1000 genomes]
rs6988808	0.92[EUR][1000 genomes]
rs6988812	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6997003	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6997127	0.95[ASN][1000 genomes]
rs6999454	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7009705	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7018162	0.94[ASN][1000 genomes]
rs73587624	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73587627	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73680321	0.84[EUR][1000 genomes]
rs73682549	0.83[EUR][1000 genomes]
rs73682551	0.83[EUR][1000 genomes]
rs73682552	0.90[EUR][1000 genomes]
rs73682555	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73682568	0.96[ASN][1000 genomes]
rs73682570	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7387704	0.80[ASN][1000 genomes]
rs7843701	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs900163	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958268	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9643480	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9643819	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9643820	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	esv2758159	chr8:54474589-54737473	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2759616	chr8:54474589-54737473	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54627400-54663400	Weak transcription	Hela-S3	cervix
2	chr8:54635000-54660200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:54641000-54654400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:54642000-54652600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr8:54642600-54672800	Weak transcription	Right Ventricle	heart
6	chr8:54643600-54652600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:54645200-54652600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr8:54645200-54654800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr8:54645400-54652600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr8:54645600-54654600	Weak transcription	HSMM	muscle
11	chr8:54645600-54654800	Weak transcription	Osteobl	bone
12	chr8:54645600-54655000	Weak transcription	NH-A	brain
13	chr8:54645600-54671400	Weak transcription	NHLF	lung
14	chr8:54645800-54652600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr8:54646000-54672600	Weak transcription	Psoas Muscle	Psoas
16	chr8:54646800-54654400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:54647000-54654800	Weak transcription	Brain Angular Gyrus	brain
18	chr8:54647200-54666600	Weak transcription	Brain Substantia Nigra	brain
19	chr8:54647600-54652400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr8:54647600-54654400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr8:54647600-54654800	Weak transcription	Fetal Kidney	kidney
22	chr8:54647600-54661600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr8:54647600-54666600	Weak transcription	A549	lung
24	chr8:54647800-54654200	Weak transcription	Brain Anterior Caudate	brain
25	chr8:54647800-54654800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr8:54647800-54654800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr8:54648000-54652600	ZNF genes & repeats	GM12878-XiMat	blood
28	chr8:54648000-54654200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr8:54648400-54652600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:54648400-54652600	ZNF genes & repeats	Dnd41	blood
31	chr8:54648600-54652400	Weak transcription	Lung	lung
32	chr8:54648600-54667200	Weak transcription	HSMMtube	muscle
33	chr8:54649400-54652600	Strong transcription	Ovary	ovary
34	chr8:54649800-54652400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr8:54649800-54652600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:54649800-54654400	Weak transcription	Brain Hippocampus Middle	brain
37	chr8:54649800-54656000	Weak transcription	Fetal Stomach	stomach
38	chr8:54649800-54657200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr8:54650000-54652600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr8:54650200-54652400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr8:54650200-54652800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr8:54650200-54653600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr8:54650200-54654400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:54650200-54654400	Weak transcription	Esophagus	oesophagus
45	chr8:54650200-54654400	Weak transcription	Gastric	stomach
46	chr8:54650200-54654400	Weak transcription	Left Ventricle	heart
47	chr8:54650200-54654400	Weak transcription	Pancreas	Pancrea
48	chr8:54650200-54654400	Weak transcription	HepG2	liver
49	chr8:54650200-54654600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr8:54650200-54654600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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