Variant report

Variant	rs4653706
Chromosome Location	chr1:226234110-226234111
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226228777..226230781-chr1:226233649..226235450,2	K562	blood:
2	chr1:226230974..226235465-chr1:226248759..226251188,4	MCF-7	breast:
3	chr1:226232126..226234237-chr1:226235651..226237839,2	MCF-7	breast:
4	chr1:226220194..226222275-chr1:226233955..226236306,2	K562	blood:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10157179	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10753411	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799333	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10799334	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10915920	0.85[EUR][1000 genomes]
rs10915921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915924	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915927	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12128917	0.90[EUR][1000 genomes]
rs1877158	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2001307	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4477241	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4604663	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653438	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653439	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653703	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653704	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653705	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426096	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426098	0.97[EUR][1000 genomes]
rs6426099	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675606	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682659	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6693325	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6701318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73100558	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7550220	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7553984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9701639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4653706	H3F3A	cis	Nerve Tibial	GTEx
rs4653706	H3F3A	cis	Artery Tibial	GTEx
rs4653706	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs4653706	H3F3A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226217800-226234400	Weak transcription	Colonic Mucosa	Colon
2	chr1:226222400-226242200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:226222600-226241400	Weak transcription	Liver	Liver
4	chr1:226222600-226242600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:226222600-226248600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:226223000-226242000	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:226223600-226234600	Weak transcription	K562	blood
8	chr1:226223800-226238400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:226223800-226242400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:226224200-226235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:226225400-226242400	Weak transcription	Fetal Brain Female	brain
12	chr1:226226000-226248000	Weak transcription	Left Ventricle	heart
13	chr1:226226600-226234200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:226228000-226235000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:226228800-226242200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:226229600-226241800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:226229600-226248200	Weak transcription	Brain Germinal Matrix	brain
18	chr1:226229800-226249400	Weak transcription	Spleen	Spleen
19	chr1:226230000-226234400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:226230000-226249200	Weak transcription	Aorta	Aorta
21	chr1:226231000-226241600	Weak transcription	Fetal Thymus	thymus
22	chr1:226231200-226242200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:226231200-226242400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:226231200-226249200	Weak transcription	Pancreas	Pancrea
25	chr1:226232000-226249200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:226232200-226249400	Weak transcription	Gastric	stomach
27	chr1:226232600-226248600	Weak transcription	Brain Substantia Nigra	brain
28	chr1:226232800-226234200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:226232800-226234200	Weak transcription	NHLF	lung
30	chr1:226232800-226234600	Weak transcription	Ovary	ovary
31	chr1:226232800-226235200	Weak transcription	Primary B cells from cord blood	blood
32	chr1:226232800-226235200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:226232800-226242000	Weak transcription	Thymus	Thymus
34	chr1:226233000-226234600	Weak transcription	HSMMtube	muscle
35	chr1:226233000-226235000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:226233200-226234600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:226233200-226235200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:226233600-226234600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:226233600-226234600	Enhancers	NHEK	skin
40	chr1:226233600-226234800	Enhancers	HMEC	breast
41	chr1:226233600-226235000	Enhancers	Fetal Intestine Large	intestine
42	chr1:226233600-226235200	Enhancers	Stomach Mucosa	stomach
43	chr1:226233600-226235200	Enhancers	HepG2	liver
44	chr1:226233600-226235400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:226233600-226235400	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:226233600-226235600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:226233600-226235600	Enhancers	Fetal Intestine Small	intestine
48	chr1:226233600-226235600	Enhancers	Osteobl	bone
49	chr1:226233600-226235800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:226233800-226234600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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