Variant report

Variant	rs73100558
Chromosome Location	chr1:226224075-226224076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226186538..226188991-chr1:226222913..226225294,3	K562	blood:
2	chr1:226221593..226225181-chr1:226248684..226250837,3	MCF-7	breast:
3	chr1:226223652..226227088-chr1:226250051..226252791,3	K562	blood:
4	chr1:226186538..226188357-chr1:226222913..226224455,2	K562	blood:
5	chr1:226205374..226207689-chr1:226223509..226225038,2	MCF-7	breast:
6	chr1:226215678..226220022-chr1:226220215..226226731,8	K562	blood:

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10157179	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753411	0.93[EUR][1000 genomes]
rs10799333	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799334	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10915920	0.83[EUR][1000 genomes]
rs10915921	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10915923	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10915924	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10915927	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11576089	0.84[ASN][1000 genomes]
rs12128917	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877158	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001307	0.86[EUR][1000 genomes]
rs4477241	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4604663	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653438	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653439	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653703	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653704	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653705	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653706	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653707	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6426096	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426098	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426099	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6675606	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6682659	0.93[EUR][1000 genomes]
rs6693325	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701318	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7550220	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7553984	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9701639	0.83[AMR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73100558	H3F3A	cis	Nerve Tibial	GTEx
rs73100558	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226217800-226234400	Weak transcription	Colonic Mucosa	Colon
2	chr1:226220400-226224200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:226221600-226224600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:226221800-226229600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:226222000-226224400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:226222400-226242200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:226222600-226231000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:226222600-226241400	Weak transcription	Liver	Liver
9	chr1:226222600-226242600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:226222600-226248600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:226223000-226242000	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:226223600-226225800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:226223600-226234600	Weak transcription	K562	blood
14	chr1:226223800-226224200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:226223800-226224400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr1:226223800-226226200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:226223800-226238400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:226223800-226242400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:226224000-226225800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:226224000-226228400	Weak transcription	Primary B cells from cord blood	blood

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