Variant report

Variant	rs7553984
Chromosome Location	chr1:226231370-226231371
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226230348..226233230-chr1:226248093..226250395,4	K562	blood:
2	chr1:226229920..226233230-chr1:226248895..226251969,4	K562	blood:
3	chr1:226230974..226235465-chr1:226248759..226251188,4	MCF-7	breast:
4	chr1:226219330..226221249-chr1:226229665..226232584,2	K562	blood:
5	chr1:226229684..226233294-chr1:226250469..226253928,4	K562	blood:
6	chr1:226227191..226229387-chr1:226231230..226233300,3	K562	blood:
7	chr1:226227406..226229526-chr1:226230036..226232756,2	K562	blood:
8	chr1:226188139..226192155-chr1:226228386..226234051,6	K562	blood:

No data

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];0.98[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915924	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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];0.99[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	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653707	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426096	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426098	0.97[EUR][1000 genomes]
rs6426099	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6675606	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682659	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6693325	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6701318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73100558	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7550220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701639	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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
rs7553984	H3F3A	cis	Esophagus Mucosa	GTEx
rs7553984	H3F3A	cis	Nerve Tibial	GTEx
rs7553984	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs7553984	H3F3A	cis	Artery Tibial	GTEx

Chromatin state (count:33 , 50 per page) page: 1

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	chr1:226225200-226232200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:226225400-226242400	Weak transcription	Fetal Brain Female	brain
13	chr1:226226000-226248000	Weak transcription	Left Ventricle	heart
14	chr1:226226600-226234200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:226228000-226235000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:226228400-226232000	Enhancers	Primary B cells from cord blood	blood
17	chr1:226228400-226232200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:226228800-226242200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:226229600-226241800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:226229600-226248200	Weak transcription	Brain Germinal Matrix	brain
21	chr1:226229800-226249400	Weak transcription	Spleen	Spleen
22	chr1:226230000-226234400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:226230000-226249200	Weak transcription	Aorta	Aorta
24	chr1:226230800-226231400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:226230800-226231600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr1:226231000-226231400	Genic enhancers	Primary hematopoietic stem cells	blood
27	chr1:226231000-226231600	Strong transcription	Brain Substantia Nigra	brain
28	chr1:226231000-226232600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:226231000-226241600	Weak transcription	Fetal Thymus	thymus
30	chr1:226231200-226232000	Weak transcription	Thymus	Thymus
31	chr1:226231200-226242200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:226231200-226242400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:226231200-226249200	Weak transcription	Pancreas	Pancrea

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