Variant report

Variant	rs4653438
Chromosome Location	chr1:226221390-226221391
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 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	chr1:226220291..226223150-chr1:226268993..226271694,2	MCF-7	breast:
5	chr1:226220237..226222759-chr1:226249970..226252556,2	K562	blood:
6	chr1:226220194..226222275-chr1:226233955..226236306,2	K562	blood:
7	chr1:226190304..226192131-chr1:226220799..226223499,3	K562	blood:
8	chr1:226215678..226220022-chr1:226220215..226226731,8	K562	blood:
9	chr1:226219248..226223033-chr1:226239868..226243673,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000225518	Chromatin interaction
ENSG00000272562	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	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753411	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[EUR][1000 genomes]
rs10799333	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915920	0.84[EUR][1000 genomes]
rs10915921	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915923	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915924	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915927	0.90[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	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001307	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4477241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4604663	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4653439	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653703	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653705	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4653706	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653707	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6426096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426098	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426099	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6675606	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6682659	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[EUR][1000 genomes]
rs6693325	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6701318	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73100558	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550220	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7553984	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9701639	0.85[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
rs4653438	H3F3A	cis	Nerve Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226215000-226221400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:226216400-226222200	Weak transcription	Brain Substantia Nigra	brain
3	chr1:226216600-226222000	Weak transcription	Placenta	Placenta
4	chr1:226217600-226221400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:226217600-226222200	Weak transcription	Liver	Liver
6	chr1:226217800-226221400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:226217800-226234400	Weak transcription	Colonic Mucosa	Colon
8	chr1:226218200-226221400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:226218200-226221600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:226218200-226221600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:226218200-226221600	Weak transcription	Stomach Mucosa	stomach
12	chr1:226219400-226222200	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:226219600-226221600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:226220200-226221400	Enhancers	Primary B cells from cord blood	blood
15	chr1:226220200-226223800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:226220200-226224000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr1:226220400-226222000	Weak transcription	HSMMtube	muscle
18	chr1:226220400-226224200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:226220600-226222000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:226220800-226222000	Weak transcription	Brain Anterior Caudate	brain
21	chr1:226221200-226221600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:226221200-226222000	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr1:226221200-226222200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr1:226221200-226222600	Enhancers	K562	blood
25	chr1:226221200-226223000	Enhancers	Primary B cells from peripheral blood	blood

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