Variant report

Variant	rs4653439
Chromosome Location	chr1:226222052-226222053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226188590..226191989-chr1:226218669..226223499,6	K562	blood:
2	chr1:226219722..226222204-chr1:226248107..226250349,2	K562	blood:
3	chr1:226220872..226223781-chr1:226226521..226228169,2	K562	blood:
4	chr1:226221612..226223515-chr1:226226689..226228264,2	MCF-7	breast:
5	chr1:226221593..226225181-chr1:226248684..226250837,3	MCF-7	breast:
6	chr1:226220291..226223150-chr1:226268993..226271694,2	MCF-7	breast:
7	chr1:226220237..226222759-chr1:226249970..226252556,2	K562	blood:
8	chr1:226220194..226222275-chr1:226233955..226236306,2	K562	blood:
9	chr1:226190304..226192131-chr1:226220799..226223499,3	K562	blood:
10	chr1:226215678..226220022-chr1:226220215..226226731,8	K562	blood:
11	chr1:226219248..226223033-chr1:226239868..226243673,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000225518	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10157179	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753411	0.94[EUR][1000 genomes]
rs10799333	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799334	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915920	0.84[EUR][1000 genomes]
rs10915921	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915923	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915924	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915927	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11576089	0.85[ASN][1000 genomes]
rs12128917	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1877158	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001307	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4477241	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4604663	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4653438	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653705	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4653706	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653707	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6426096	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426098	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426099	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6675606	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6682659	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6693325	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6701318	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73100558	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550220	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7553984	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9701639	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4653439	H3F3A	cis	Nerve Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226216400-226222200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:226217600-226222200	Weak transcription	Liver	Liver
3	chr1:226217800-226234400	Weak transcription	Colonic Mucosa	Colon
4	chr1:226219400-226222200	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:226220200-226223800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:226220200-226224000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:226220400-226224200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:226221200-226222200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr1:226221200-226222600	Enhancers	K562	blood
10	chr1:226221200-226223000	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:226221400-226222600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:226221400-226222600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:226221400-226222800	Enhancers	Fetal Lung	lung
14	chr1:226221400-226223000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:226221400-226223600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:226221400-226223600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:226221400-226223800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:226221400-226223800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:226221600-226222400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:226221600-226222600	Enhancers	Fetal Intestine Small	intestine
21	chr1:226221600-226222800	Enhancers	Fetal Intestine Large	intestine
22	chr1:226221600-226222800	Enhancers	Stomach Mucosa	stomach
23	chr1:226221600-226223000	Enhancers	NHDF-Ad	bronchial
24	chr1:226221600-226223800	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr1:226221600-226224600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:226221800-226222200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:226221800-226222800	Enhancers	Osteobl	bone
28	chr1:226221800-226223000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:226221800-226223000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:226221800-226229600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:226222000-226222200	Enhancers	Placenta	Placenta
32	chr1:226222000-226222400	Enhancers	Fetal Brain Male	brain
33	chr1:226222000-226222600	Enhancers	Brain Angular Gyrus	brain
34	chr1:226222000-226222600	Enhancers	Brain Anterior Caudate	brain
35	chr1:226222000-226222600	Enhancers	Brain Cingulate Gyrus	brain
36	chr1:226222000-226222600	Enhancers	HSMMtube	muscle
37	chr1:226222000-226222600	Enhancers	NH-A	brain
38	chr1:226222000-226222800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:226222000-226222800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:226222000-226222800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:226222000-226222800	Enhancers	Duodenum Mucosa	Duodenum
42	chr1:226222000-226222800	Enhancers	HSMM	muscle
43	chr1:226222000-226223000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:226222000-226223400	Enhancers	Adipose Nuclei	Adipose
45	chr1:226222000-226223800	Enhancers	Primary hematopoietic stem cells	blood
46	chr1:226222000-226224400	Enhancers	Primary monocytes fromperipheralblood	blood

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